Like TG Twinkie said above, just use 1/2" PEX through out. From what you described, it sounds like you AS was plumbed with 3/8" copper, which is pretty small, but things like the water heater only have 1/2" fittings on them. So the inlets/outlets were done in 1/2" and it was then reduced down to 3/8". As you'll be doing all 1/2", its largely irrelevant.
As a side note, make sure you stick to one system. As a General Contractor, I've done both the expansion type and the crimp type, and have the tools for both. But most times, including my own home, I use the system from Home Depot.
Buying a system from a Plumbing supply house is more "professional", but some supply houses only sell to the trade, can sometimes be more expensive if your not a regular with an account and are very rarely opened weekends or past 5:00pm. Home Depots or Lowes or Aces are all over the country and usually stock the same parts.
Good luck and have fun.