I don't know what kind of underhood fuse box you have, but in this situation, the general approach is to power the LS as a standalone system. Integrating it into an original harness is asking for trouble as the wiring is old and may very well have been hacked on through the years. If you haven't already, I would suggest buying a fuse/relay block like this (water resistant):
https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1
Then, using the info from LT1Swap, build this fuse block. You should never have any connection to the battery without a fuse.
My knowledge of working with an original harness in a square body is limited, so I will offer you what I can on a few connections. Looking at the pinouts on LT1Swap.com, the wires that you need to identify and connect externally are highlighted in blue. These wires will not be removed from the X connectors, but they should be loose somewhere as they should be cut from the donor vehicle fuse box. The wires highlighted in yellow can be removed from the X connectors and removed from the harness entirely. Some notes on the blue highlighted wires:
-Brake switch signal-runs to your brake switch under the dash. Gen IV's need 12v signal when brakes are applied. Make this easier by buying this switch if you don't already have this 4-prong style switch:
https://www.psiconversion.com/produc.../KIT-1002.html
-High speed and low speed cooling fan relay controls-run to your cooling fan relays (ground signal). Below is a a GM cooling fan wiring diagram that matches how your Gen IV functioned in stock form.
-Starter solenoid (purple)-I believe this can be independent of the LS harness, in that it just needs to get from the starter solenoid to the key switch.
-Fuel pump-your LS harness should have a single wire that provides a 12v signal when the PCM says it's time to run the fuel pump. This wire will run to the fuel pump relay and power will be distributed from there. The rest of the wiring for the fuel pump should be independent of the LS harness and new. I would do 10 gauge due to the demand of the fuel pump and also the length.
-Wires that require ignition or battery hot, run those through fuses.
-MIL control-this wire provides a ground signal when the PCM decides that there is an issue. This is your check engine light.
I know this is a lot of info. I would recommend reading all the info on LT1Swap and browsing through this LSX Swap forum. Any other questions, let us know.
Dual Fan GM Schematic.pdf