[hatzie]

Programming the 6.0L LQ4 or LQ9 PCM to operate stand-alone for a Manual transmission or early mechanical Automagic is the same as programming the 5.3L LM7 PCM for the same. Other people have done this so tune files that you can peruse to see how the other guys did it should be easily available.
You can change from 4x4 to 2x4 just as easily.

Programming...

Programming the PCM to GM defaults for the donor engine and settings you want would be my first step. Pick a VIN for the LM7 that has a manual transmission and 2WD. Who cares what the VIN in the PCM is as long as it has the options you want so you can write the proper baseline Calibrations to the PCM. If you look at my 2005 Silverado thread there's info on how to do this using a Chinese WiFi MDI or GM VX Diag or some other SAE J2534 interface and the AC Delco TIS web applet. You will have to pay $40 for a 2 year Delco TIS subscription... HP Tuners MPVI2 doesn't act as a J2534 interface.

First set the PCM to an original GM baseline via TIS then start tuning it. Why do I say this?
HP Tuners, and likely others, business model is geared toward servicing professional "tuner" shops. Hobbyists appear to be an annoyance to them. The "single PCM" credits you buy are supposedly licensed to one PCM. There is no un-changeable ESN in the PCM so "Licensed to a PCM" is not an accurate description of how they are determining what PCM is connected to the interface. As near as I can determine they use the PCM Operating System, VIN, and several other software settable items to determine what PCM the interface is connected to. These software settable items could be changed by an update from TIS. If you change/update the OS or configs from TIS after you register HP Credits to the PCM it will void the credits even tho you haven't changed the hardware. They will make you buy two more credits for the "new" PCM. They are pretty hard nosed about it too.

I believe the LQ4 and LQ9 cranks were bored for a pilot bearing. You just have to get one that matches the input shaft on your transmission.

The LS bellhousing is missing one of the RH bolts but the old Chevy bellhousing will still bolt up.

The flywheel and possibly the transmission input shaft length is where it starts to get fun. The distance of the flywheel mounting surface of the crank to the bellhousing mounting surface differ from the old Chebby smallblock and big block engines.