Keep your stock vortec harness and don't just rip it apart like most. Remove it from the truck in one piece. You'll need to remove components like the injectors and stuff you know the LS1 harness already has because it'll run off of the new 5.3 pcm. I have a 98 manual so I can guide you with what you need to remove. You'll want to keep things like the oil pressure/fuel switch that bolts on the back of the block and it will be moved down to the oil filter bypass on the side of the block by the oil filter which will need to be tapped to 1/8" pipe if I remember correctly, transmission wiring, gauges, etc.......you can use HPTuners to set the tach resolution to 3 to keep from buying a tach module. You'll want to keep the vortec plug for the altenator because it will plug into the 5.3 altenator for the gauges. All of your gauges will work correctly if you don't destroy the vortec harness and I can't stress that enough. You can add the electric fan relays, A/C and fuses with a small stanalone harness like I did which was very simple. You'll need a weather pack terminal connector kit if you want to make factory connections. Remember to disconnect the vortec harness at the C100 connector on the fire wall, unplug the connectors below the cruise control unit and unplug the blower connections in the cab on the passenger side and pull them through the firewall then the whole harness will release. Wherever you mount your PCM will dictate the length of your standalone harness the will need to be added.

Good luck!