I just swapped my NV5600 out for an Allison. Here's some of the things I've found:
NV5600's are worth a chunk of change. I sold mine for almost $4k (ferramic clutch, flywheel, & transfer case). Try to work as many of the auto donor parts into the deal as possible (column, shifter, linkage, cup holder, transfer case, & drive shafts if going to a Dodge auto, etc. )
You'll need to swap to a 2002 auto ECM. I believe a 2001 ECM won't give you an oil pressure reading in the cab. Manual ECMs have an anti-stall feature which at a stop, senses the torque converter as a load, then increases fuel, then tries to bring it back to idle, then does it all over again, and again. It makes for a romp, romp sensation at a stop and is also really bad in reverse. The whole truck shakes like a top fuel dragster, kind of sounds like one to. Also, brake pedal effort to stop, and keep stopped is extreme because of the anti-stall and the truck really wants to take off, holding the brake pedal down at a stop was similar, if not harder, than holding my old clutch down. I found I could sometimes fool it if I just coasted to a stop, but a quick stop, forget it. The auto ECM cured all this. By the way, the auto ECM didn't seem to have any problem running my HO pump.
2001 & 2002 manuals had cruise controls that were 100% ECM controlled. So I lost my cruise going to the auto ECM. Auto's have a vacuum speed control servo manuals don't have. So I've now installed the servo & bracket (under driver's side battery box), servo to throttle linkage in the APPS, and a vacuum line. Still no cruise control! What I've been told is that I also need an auto PCM. I'm going explore getting it reflashed as well as picking up one from a junk yard. I'll let you know on that soon.
I didn't actually do the physical Allison swap, so I can put you in touch with that person if you're interested.