I am undertaking this project right now. I live near about six pic-ur-parts so I have been able to get a rear end ($120) and 5 sp9$150), driveshaft(50), pedals, hydro-boost ($90) all for good prices relatively easily. I paid $500 for a super clean intake with brand new throttle cable. I think $200 for cobra valve covers, front engine cover ($150), then there was the alternator (80) , the alt bracket (60), the coolant intake pipe ($180), Then i realized I needed all the ABS system($140) , including lines because the v6 non-abs has different lines.
I decided to freshen up the DOHC engine (Junkyard Aviator), so about $1300 for machine work including valve job, just hone and re-use pistons, but at least $350 in main and head bolts. Of course I want it to last so I got new lifters and followers, around ($600), timing set ($500), plus all new gaskets and seals.
I got the computer and its harness, the engine bay fuse block harness, and dash harness from ebay for over $500. I needed the dash harness because mine is a 2000 and they changed some things in 2001, and now I want everything 2003. I am also swapping to a 2003 dash, ($80). The GT flywheel I scored needed re-surfacing, ($60), driveshaft was balanced with new U-joints installed ($180),
I am delayed right now because: First I ordered the wrong rings. For 03-04 some 4.6 have a top ring of 1.2 thickness, not 1.5. Next- piston rings were backordered, then I ruined a set because Chiltons/Haynes says to gap end of rings to .039. That is wrong. They should be half that big of gap. I'm glad I decided to doubled check before I sent it.
So it can be done. It has been alot of work and driving around. I am wishing I would have bought a Bullet for $5000 I was looking at. or putting a turbo kit on a V6. I see why racers still use SBF because they are way cheaper to rebuild.