disclaimer: this is going to be an incredibly long post because i see you're having a couple problems and are definitely putting forth effort. i hate to see large amounts of safrole go through so much labor only to go to waste. it breaks my heart
so i'll do the best i can to shed some light.
ok i'll start at the beginning, the peracid oxidation and chronologically work my way down, covering as many helpful details as possible. these details are perhaps overkill but i think it might help you get the jist of things. when referring to the product of the peracid oxidation i'm going to refer to the glycol as your product, but the product of the peracid oxidation actually depends. there are 3 possible products of the peracid oxidation and all 3 are usable/desirable, in other words all 3 of these products - when tossed into the pinacol rearrangement - will react to completion to yield mdp2p (i'm speaking generally, of course some of all 3 will react to form by-products in small amounts too but i'm not going to go there). if you run the unbuffered peracid oxidation then the reaction is quite acidic and has more of a reputation to have the potential to create more by-products than the buffered reaction due to this reason. in my personal opinion, and in retrospect, i would recommend that you just do the unbuffered peracid oxidation even though it's yields are traditionally a little lower than the buffered. the reason for that is to not complicate things too much, just shoot for success for now even if the yields are lower than the buffered route. once you have success a couple times or however many times it takes for you to feel comfortable with these reactions, then go ahead and run the buffered and focus on improving yields. but for now let's focus on success, then focus on getting more comfortable with it. once you know you have it down then focus on improving yields and efficiency.
the unbuffered peracid oxidation will yield the epoxide only as an intermediary compound, due to the solution being so acidic, the epoxide always reacts to form the glycol. once the peracid (performic or peracetic) oxidizes your product, the peracid no longer has that extra oxygen so your peracid has now returned back to being the original acid (formic or acetic). due to the presence of excess acid (formic or acetic), some of your glycol will become an ester. if you used peracetic acid, meaning you will have acetic acid in the solution once it loses that extra oxygen, then the name of the ester is isosafrole acetyl glycol. if you used performic acid which leads to formic acid within the solution, then the name of the ester is isosafrole monoformyl glycol. so for the unbuffered reaction you get a mix of the glycol and the glycol ester, which is fine as both will yield mdp2p.
the buffered peracid oxidation can actually yield the epoxide as the end product. this is because the buffered reaction doesn't have the excess acid that the unbuffered does. if you goof up the calculations while scaling up/down your reactants and get the ratios of acid/base wrong then that will change the outcome. but let's say you run the buffered reaction to perfection, you will not get the ester at all because there will not be enough excess acid for that to happen. not only that but there will not be enough excess acid for all the epoxide to become the glycol, some of the epoxide will become the glycol but not all of it, the amount of excess acid will be the limiting reagent in that little equation. so the buffered reaction will yield a combination of epoxide and glycol, the ratio of epoxide to glycol depends and isn't worth discussing because both work just fine to yield mdp2p.
for the peracid oxidation it sounds like you have it down now. you pulled off the reaction and fractal filled you in on how it's supposed to be worked up which was with water washes, back-extract from the water washes per jon, pool all the dcm together and distill off the dcm, leaving the somewhat crude glycol which is fine for the next step. don't distill the glycol, the only distillation for this reaction will be distilling off the dcm at atmospheric pressure. i had completely forgotten that chromic instructs a 5% NaOH wash after the peracid oxidation, it's been some years since i've read his write-up.
it sounds like you're good with running the pinacol rearrangement with no problem, but you skipped basic water washes, understandably due to the problems it caused when you washed the glycol. but the pinacol rearrangement is the reaction that requires the basic water wash to help neutralize residual acid. water is fairly soluble in dcm, because of dcm's dielectric constant being higher than other non-polar solvents such as toluene/xylene. i'm not saying to use toluene/xylene, definitely stick with the dcm. i just wanted to let you know that since there will absolutely be water present in the dcm, and that since the water is very acidic, that means your dcm will be containing some of that acidic water. since you didn't do a base wash your dcm had acidic water in it, some of it probably co-distilled with your dcm but i'd expect some to remain behind with your crude mdp2p. then you went to vac distill the crude mdp2p with high heat and the presence of acid, so there goes your mdp2p :\ so what you want to do after you extract the crude mdp2p with dcm, you'll want to wash the dcm 3 times with a 5% NaHCO3 solution. for the first 5% NaHCO3 wash just gently rock it back and forth, do a thorough wash but try to be gentle and patient, the reason for this is to avoid a potential emulsion since you'll be making a lot of base salts during then neutralization with this wash. for the second and third 5% NaHCO3 washes go ahead and shake vigorously. now you'll want to do one more wash before distilling anything. wash it one last time really well with a saturated brine solution, do 2 brine washes if you want. the purpose of these washes are to remove any residual small amount of NaHCO3 that is present in your dcm from the basic washes. if you want, you can back-extract from those washes with fresh dcm but if you do back-extract then you'll want to take the dcm you used to back-extract from the washes and wash that dcm with a saturated brine once. THEN pool that back-extracted dcm with the rest of your dcm from your 3 extractions earlier. it sounds very redundant i know and it is very redundant. but my rule is to be very anal about making sure there is no presence of excess acid or base with your crude mdp2p, it's good to be very anal about that so there is less risk of polymerization and side reactions happening, cleavage of the md bridge, etc, from high heat + mdp2p + acid or base. the reason for the one saturated brine wash on the dcm you use to back-extract from the washes with, is because those washes when pooled together is a weak NaHCO3 solution full of impurities and base salts. you want to rule out any of that NaHCO3 getting into the dcm you use to back-extract. yeah NaHCO3 is a weak base and yeah there isn't much in those washes but it's better to just be anal about it b/c you've put in too much work to play russian roulette over a preventable mistake. since you're just looking to find success your first time, my opinion is to not do the back-extraction for the pinacol rearrangement this time around. just do the reaction, extract, do the washes, then distill off the dcm, then vacuum distill the crude mdp2p. once you've had success and have the hang of all this, then you'll work towards upping your yields and then you'll worry about the back-extract. just keep in mind about dcm and water being more soluble in one another than other non-polar solvents, so you're aware of dcm's ability to have water in it and since it has water in it, it can have whatever is dissolved in the water as well and carry some of that over to the dcm. the other side to that is that some of the water you use for washes, etc, will have some of your precious dcm in it as well. so if you use a total of 1000ml dcm to extract with, once you go through washes, etc, and distill off the dcm you may notice you only get 800ml dcm back. that 800ml dcm is a completely made up number i used as an example only, that example isn't based on solubility vs volume calculations or anything, so the real amount may be nowhere near that number, it's just an example. so if you're losing dcm due to some of it being in the water that is being discarded, then you'll know some of your mdp2p will be discarded with the water washes too. but that's ok, just focus on success for now. once you're successful then go back and try back-extracting, etc.
a note about the basic wash that's part of the work-up after the pinacol rearrangement: the NaHCO3 solution will do just fine for neutralizing the acidic reaction solution as long as you use enough of it, no need for NaOH. you can use 5% NaOH here as chromic instructs but i'd err on the side of caution and just go with NaHCO3 because it's a weaker base. why does that matter? because if there's residual NaOH present in your crude ketone then you vacuum distill it, NaOH has a bad reputation for polymerizing mdp2p when heated together.
VL is absolutely right. regarding the washes it's best to trust your eyes over the instructions. if it says 3 washes but your 3rd wash still removed color then keep going until the washes aren't removing any color. what VL says about byproducts reducing your yields is dead-on. if you do a sloppy work-up, half-ass the washes, then you're crude mdp2p will be much more crude and impure than it should be. what that means is when you heat it up really hot to vac distill it, side reactions can occur and even worse, polymerization or tar formation can occur, once that happens - that shit is so thick it will trap the mdp2p from distilling over.
you shouldn't be getting any red colored distillate at any point. the distilled dcm should come over clear, perhaps a little cloudy if there's water in it. isosafrole should distill over clear, at worst with a yellowish tinge. if it has a yellowish tinge (a more regular yellow color, not the fluorescent type of yellow associated with mdp2p) then that's most likely from some unreacted safrole which is present, that's ok if there's a very small amount of unreacted safrole present i wouldn't sweat it. mdp2p's color when pure is disputed somewhat but the general consensus of 99.9% of us will probably agree that the mdp2p should distill over anywhere from a fluorescent yellow color - to a fluorescent yellow with a slight antifreeze green tinge depending on your lighting - to a yellowish/greenish color that might look more greenish than yellow. if you're distilling over fractions that contain the red/purple by-products that VL mentioned then you're most likely distilling way too fast - applying way too much heat and you're driving the impurities over. these impurities can co-distill with water to some extent, but you definitely should not see any distillate coming over that is anything resembling a reddish to purplish range of colors because all water will be removed under the vacuum atmosphere at a much lower temp then safrole/isosafrole/mdp2p, however if you go crazy with the heat then you might make the temp spike so high and fast that you just distill all those fractions over together as one big mess. distillations suck i know. distilling dcm is a piece of cake cuz it's so volatile but aside from that, the distillations take a long time and you have to do a lot of them but you need to be patient and be sure to not go crazy with the heat knob on your hotplate. vac distillations are even more of a pain in the ass cuz they take even longer. you just need to get good and accurate and being able to zero in on the desired temperature and knock those distillates over one fraction at a time. after doing it enough times you'll probably get a good feel for what heat setting corresponds with a particular temperature scope for water baths and then a different scope for oil baths, unless you use your hotplate in a place where the ambient temp fluctuates of course. in my opinion it's fine to overshoot the desired bp temp to drive over that last little bit of mdp2p during a vac distillation because i hate when there's that last little bit of fluorescent yellow in the distilling flask and doesn't want to come over, just don't go too crazy with it. you want to keep track of the temp of your bath and also your distillation thermometer. download truecrypt to make an encrypted volume and keep lab notes, store them in the encrypted volume with very strong encryption. lab notes are incriminating but also very helpful when trying to troubleshoot especially if you're trying new reactions that you're not experienced with yet.
good luck