I would agree, those are two things I would look at in GREAT detail before starting this. I was planning on the v8 thing at first, but then decided on the turbo, but I would have done the v8 if I needed to cut the hood. I spent a weekend just doing all the math, measurments, and parts research: It was time well spent. I can't imagine the v6 being any taller than the 2.3 efi, and you might not have parts you can swap out to help with that either.
Take a good look at any 3.8 donor you plan to use, they are PRONE to head issues.
I don't know if the have the same bell bolt pattern.
The oilpan will need to be a front sump, and not only that, with the short v6, you might have to move the engine forward to give ROOM for a sump. This will bring tranny and driveshaft issues too, and if you want a standard, it could be worse. I am sure that you would need a full custom motor mount set up of some sort.
I have never seen a pinto with a 3.8, but I like things like that. Take a look in the FAQ section for info on an efi swap, most of the same stuff will apply. The best bet is to get a good running full car as a donor. Trust me, it makes things much easier, as does a welder, torches, and air tools.
Go for it,
Bill