120k on these engines is not that much, and if you are wanting to supercharge it, you could have shop perform a leak down test and compression test to see how healthy your engine is. I would have no problem superchargin a 4.6L with 120k on it. This is just my opinion.
If you are set on rebuilding, after pulling the engine, you would need the block cleaned up, heat tanked, re-bored, re-honed, new pistons/rings (at least) to match the new bore, seals, freeze plugs, oil pump, your heads should be cleaned up, sounds like you want a forged rotating assembly to handle the supercharger...after all that, you could have bought a long block already assembled from Ford Racing/MMR/MHS or another reputable
shop. Saves you time and in most cases money.
You could also find a used engine on ebay/craigslist/junk-yard and have that one rebuilt that way your car is not out of commission while you're engine is being built.
As far as rebuilding the tranny, kind of the same thing as the engine. Will this thing be a track car? Cruise car? If it not gonig to be a track only car, the stock transmission may be fine for quite awhile.
The real question is...What is your budget???? and What power level are you seeking?
EDIT: Don't forget suspension/braking/chassis bracing