I've got a LS2 with a 411 PCM in my '98 truck. I completely ditched the vortec PCM. I used a 5.3 harness from a 2001 truck, had to cut and splice to match it up to the fuse panel, to the connector on the firewall, and had to run some miscellaneous wires here and there. The 411 PCM outputs the correct VSS so that ABS and speedometer will work. Tach resolution can be changed in the PCM so the tach reads correctly also. I believe I used High 3 Low 2 or vice versa on the tach resolution. The only thing that will not work on the '98 is the fuel guage. I'm running a programmable Autometer gauge that works off the stock fuel sender. Works perfectly. Also, if you do the motor mounts correctly, you will not need custom parts anywhere, transmission lines, driveshafts, exhaust etc will all line up and be bolt on parts. Most conversion motor mounts move the engine back to far so everything needs to be custom made. My truck has been running for almost two years with zero issues.
Old: 1998 K1500 White ext cab stepside, vortec 350. Stock besides Volant intake.
New: 1998 K1500 with stock LS2 besides LQ9 truck intake and 8.1L Marine injectors. Dynotuned, 350rwhp, custom 3.5" exhaust, '02 F-Body Racetronix fuel pump setup. All wiring, exhaust, motor brackets done in shop.