So does anyone know how difficult it would be to get a 3.8 V6 from a 99' or new into a 66' I6. And do you think I would have to change out the rear end?

 

i dont know anyone who has done that, but there are lots of considerations
engine mounts will be different
exhaust would need to be customised
wiring
engine management computer to be fitted
gearbox mounts
gearbox to tailshaft to diff custom
radiator custom
radiator hoses non standard

you wouldnt necessarily have to change the diff.

you'd also need some good brakes and handling mods to handle the extra go!!! In all, a massive and expensive undertaking.

personally, i think it would be heaps cheaper and easier to swap to a 289 or 302. Cheaper again to buy one already done.

I'd start with one of the RestoMod sites who may have done something like what you want to do.

 

I tend to agree with aussie66. But my 96 V6 gets 27mpg on the hwy with power to pass.
I know the later 4R70W tranny will fit perfectly. I think the oil pan would be the first issue to deal with and then fabricating motor mounts.
There is plenty of room to do it. Just a lot of work.