I would certainly hope that he charges the NewEgg/Amazon price for the part in addition to a healthy hourly wage, and transport costs if there are any.

If he's keeping a stock of a lot of parts it can be worth a markup. But in general the cost of having someone buy a part and install it vs. buying the part yourself and paying someone to install it should be pretty close.

I've never actually needed repairs to my own computer. I live in a very strange vacuum where things tend to not-fail around me. I've mostly chalked it up to the "developer looking over your shoulder" effect.