of the beam is 10 cm or about 4"(3.93) so anything that is less than that and not 1/4 wavelength should be fine... if you look on the links, you'll find pages where they bored holes into the top for a camera. You can also get a rat shack mw power meter and test the hole.. also wrapping a bit of screen around the glass ware coming out should take care of any incidental radiation.
The issues aren't about a lot of power here... you usually have to put a beaker of water in the oven to get the power down to 400 watts or so... more is not better in this case...
I bought the sams guide to repairing microwave ovens to figure out how to modify them...it's very helpful...
re: thyratrons... well, why is a question, but also you would have to look at the standing wave patterns and resonances created by your multiple emitters in a closed space... looks like very nasty 3rd order calculus to me, as you could end up with junk if the beam front reinforces into one of your emitters generating a lot of feed back that fries everything... Just get a cheap 500 watt college dorm model at a garage sale and get on with chem instead of physics...
Infinite Radiant Light - THKRA