I've done the 6.2 diesel automatic --> 5-speed swap twice (see both threads in my sig. line).
To answer your first question, a 1990 4WD TH400 should have the same flange-to-flange length & spline count as a 1993 NV4500. I did the same swap to my '86 Blazer and my crossmember still lined up with the original frame holes. No drilling required (for that portion). Your truck has a newer style of crossmember, but the transmission mount geometry is identical.
I also retrofitted a stock squarebody hydraulic clutch bell housing (1985 and newer) to my early-style NV4500. It does require drilling, but aside from that it allows you to stick with 100% stock GM squarebody clutch parts. No funny hydraulic adapters, no having the clutch slave wedged against the oversized diesel starter motor.
I've run into many (probably most) of the problems one can encounter swapping from TH400 --> NV4500, so feel free to ask more questions as you go.