Great father son project - you mention you are both learning as you go - dad used to say "you can't learn any sooner" so go for it! As far as blowing a day running back and forth for parts, it does get frustrating feeling like spent more time running for parts than actual work. Get yourself a list going and when you come to a standstill for one part related to one task, jot it down, then start down another task till you hit a roadblock there, then jot down what you need to get that going again. Don't "burn daylight" doing parts runs - get as much done with your daylight as you can and do the parts run in the evening after you get cleaned up and the tools put away.
Thanks!!! Yeah... I just ordered a new clutch, oil pump, water pump, and thermostat from Rock Auto. Their prices are the best. I ordered all AISIN stuff witch is basically Toyota OEM stuff.