Why would you do this when there are plenty of 4.6L Tbirds to be had for cheap?
1) While the 4.6L donor vehicle is almost certainly a 95-97, I sincerely hope that the host car is also of a similar vintage (vs an 89-93 early model). Otherwise, this OP is in for a ton of work as there are all sorts of little chassis differences in how they were wired (ex: fuel relay in trunk vs. a CCRM, signal to activate the ECU, etc) even if the ABS system is separate from the ECU in the early and late model cars. I know about all of these challenges when I swapped my 95's 3.8L for a 5.0 from an 93 model.
I did this because i already had $1500 into a rollcage in my chassis and I already had a manual swapped in so I was committed the the SBF bellhousing pattern.
Key Suggestion: Since the Op has already purchased his donor, I would HIGHLY recommend that he pickup the host car's shop and the EVTMs for both the host and donor cars. All of these manuals can be had for $10/ea on eBay most days of the week.
* you are gonna have to swap the transmission as the 3.8L uses a different bell housing pattern than the 4.6L even if they are both 4R70W (assuming 95-97 cars)
* You are going to have to swap gauge clusters (or at a minimum, the speedometer from the V8 needs to go into the V6). This is because they measure a different # of tics of the RPM signal so your RPMs will be off if you use the entire V6 gauge cluster.
- In going from the V8 to V6, I've swapped just the speedometer gauge (it plugs in/out) but the front clear plastic cover didn't fit well. I didn't care (because racecar) but this may pose a problem for you that you'll have to figure out.
- I also know that the 97 gauge cluster surround is slightly different so if your donor vehicle is a 97 and your host vehicle is a 95-96, I'm not sure how much you'll have to swap over to make everything fit just right (just the cluster+plastic surround or more).
* The rear axles are thicker with a V8 vs a V6 N/A. You'll wanna swap them over unless doing so means you'll lose ABS (ex: if the donor vehicle didn't have ABS but the host car does so the sensor ring isn't on the thicker axles).
* Front/rear swaybars are different from V6 to V8. You'll want to go with the thicker ones.
89-97 Thunderbird Anti-Sway Bar sizes
* Front/rear spring rates are different from V6 to V8. Your best bet is to replace them while your car is in pieces but if you are trying to do it on the cheap (which I think you are), you'll probably wanna to go with the least worn components. Just keep them in matched pairs and FWIW, stock rear springs should be the same for all 3.8L N/A and V8 cars.
Thunderbird Lowering Springs
* Exhaust is different (3.8L/5.0L stock exhaust manifolds dump at the same points but 4.6L cars are different) so you'll need to use the donor vehicles exhaust (or fabricate a new exhaust).
* Double check the wiring going to the transmission to make sure it's the same. I had to modify this wiring b/c I want to a manual but I'm not sure going from auto to auto. This is more fun if your host car had a non-ECU controlled transmission (AOD) and you are moving to an ECU controlled 4R70W.
* If your host car is an early model with a digital dash, good luck. I noticing the dash wiring is substantially different from an analog to a digital car even of the same year.
Bottom Line: I wouldn't do it. if the new purchase is only a donor/parts car, I'd sell both and just buy a servicable 4.6L powered MN12 if that's what you really want.