I'm doing this same thing right now. See the link to my build in my signature.
My bike is going to be my daily rider so I'm doing everything I can to give it the best chance of being reliable. Focusing on the engine (not the wiring, suspension etc) I took the whole thing down to individual components. Inspected everything, replaced the parts that are prone to wear, put it back together with all new seals and gaskets.
If you go this route it will not be cheap and can be time consuming. Here's the break down of what I've spent / projected to spend (i have part numbers for everything if you want them. PM me):
Primary chains (90)
HD Cam chain (30)
every o-ring (90)
primary chain tensioner (it may not look bad but trust me...it is) (80)
every seal (35)
gasket set (90)
main bearings (140) - inspect prior so you know what color you need if you need to swap them
rod bearings (90) - inspect prior so you know what color you need if you need to swap them
rod bolts - (90) - mine were way stretched
Dynoman 836 kit (500)
boring by APE (200)
head rebuild (500) - titanium retainers, new springs, ss valves, bronze guides APE
cam chain tensioner (50) - i'm going with a manual tensioner
OPTIONAL: head porting / polishing by mrieck
OPTIONAL: cam (200)
And there you have it...