I think you better consider beefing the trans. Putting a 3.9 in front of a 5.9 trans is no problem. The other way around is almost sure to die a quick death. The 3.9 tranny is the same physical size and internals BUT they used fewer clutches in the clutch packs and can't handle the extra torque for long. I once built a 904 (baby) torqueflite for myself to use with a 11 sec 360 I built. The thing worked fine until more than 1/2 throttle going into 3rd. I all ready had one extra clutch disk in 3rd and ended up on the lathe machining room for 7 (factory 4, mod 5, finally 7). After that it was fine and would bang into 3rd up to 3/4 throttle. More than that and it felt like a HD shift kit would. You'll have to decide for yourself what to do. At least put a shift kit in with higher line pressure. That's just my 2 cents.
Tranny man since 1982.