Did a auto to NV3500 manual swap on my 88. My LQ4 has an NV4500 behind it.
Get a flywheel from a 4.8 manual engine. Depending on what you are doing with the truck do not discount an NV3500. Not as good for towing as a NV4500 but they shift smooth and are probably going to be easier to find and cheaper than a 4500. As for the bell housing for an LS, it should bolt up to an earlier one minus one bolt.
For clutch are you going internal or external slave cylinder? For mounting the master cylinder the earlier years slave has two mounting holes and the later years have more of a snap in style. Go with an earlier if you can. Also some hydraulic connections on earlier clutch master and slaves can be threaded or use an o-ring and pin. Pay attention if you are mixing parts.