A lot of this depends on what time your scope will be. Basically, you can't eat for 24 hours prior to the scope. You can drink as many clear liquids as you want, and you should drink a LOT since you'll be losing tons of fluid with the prep. I wouldn't worry too much about the headache as long as you're taking in plenty of fluids; if you do get one, try a cold pack on your head (works miracles). I've found that usually the "explosion" (LOL) lasts a few hours. I'd drink the stuff and half an hour later start the tremendous joy of expelling all matter from my innards...and probably went about 50 times or so. Make sure you definitely have those baby wipes handy!
They will take biopsies during your scope to check for all kinds of goodies. Usually the best way to recover any parasites are during stool tests, which aren't 100% accurate anyway since parasite eggs are only shed intermittently in stools. But there's not really a better way to test for them (yet, anyway). They'll be able to tell if the colon is shaped normally or not as well.