Guys: I went through this exercise lsst fall with a friend of mine, trying to replace a 391 with a 390 - we couldn't make it work without major modifications. I also just posted on this very subject in the '61 - 66 forum; to save you time, here is what I said:
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The 330 is the smallest (in CID) of the FT engine family, which includes the 330, 361 and 391.
The FE motors include the 332, 352, 360, 390, 406, 410, 427, and 428.
The FT and FE motors share many similar dimensions, but they are NOT INTERCHANGEABLE without significant modifications.
The FT cranks are forged instead of cast, but the snout of the crankshaft has a larger diameter. This means the front timing cover has a larger hole and seal in it. Unfortunately, this means you cannot replace an FT motor with an FE motor not only because the front timing cover crankshaft hole on an FT is larger (the FE crank won't seal), but also because the front timing cover on an FT motor is the front engine support. (I've heard that a popular FE racing mod is to get the forged 391 FT crank, turn the snout down to FE dimensions, and use it in a 390 FE for greater reliability.)
FT rear engine mounts use the bellhousing, which has the rear engine support bosses cast into it - unlike the FE motor, which uses the side of the block for the mounts. The FT side engine mount holes are not in the same position as an FE.
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Now, to go the other way, replacing a 390 with a 391 block might be a lttle easier. I see the following issues or possible issues:
1. The side engine mounts will most likely need to be fabricated.
2. Will the clutch/flexplate bolt to the 391 flywheel?
3. The 391 distributor will have to be utilized, if I remember right, the 391 block must be bushed to use the 390's distributor.
4. The front crank seal will be an issue.
Now this is where I haven't been able to get firm hold on this issue: Would it be possible to use the FE timing cover on a 391, and get a proper fitting seal on the 391 crank?
One possible - and easy - solution may be the answer to this question: IS the 391 crank snout OD the same as the FE crank snout diameter WITH THE FE oil seal sleeve in place???
Anybody know? Any other ideas?