I'd choose based on two factors: power in, and what t-case you've got.
If you're running a hot smallblock or a bigblock, then a TH350, even when built, may not hold up. The Turbo 400 would be a better choice for higher horsepower, heavier duty use.
That said, the output shaft is different, so if your truck is set up for a TH350 now, changing to a TH400 would also mean changing the transfer case (or output shaft.)
If you are going to swap trannies, I'd try to get an entire tranny/adapter/t-case combo out of a donor vehicle.
Oh, and the T400 might be longer (this also depends on adapter and t-case) so you might need to change driveshafts.
-- A