It may have been an idea to add a little more water at the end of your reaction, so you have more fluid to work with.
As for basifying it, you DONT need pH papers. Just add a NaOH solution, a bit at a time, and swirl. The pH will bee high enough when the fluid goes milky white, and does not clear up after a few minutes.
As for the excess HCl, if this ever happens again, just evaporate, and flash with cold, dry acetone. Wait for it to cool and then pour it off, leaving the meth. It will wash away the colour and the excess HCl. You may need to wash more than once.