[franken]

We need actual voltage measurements and where they were taken to even start to guess. What's the battery voltage measured at the battery using a DVM? Same question w/ the engine idling? Same Q at 2k RPM?
Rather than an expensive wiring harness, I'd start by cleaning contacts, and fixing cheap ground connections.
If a certain thing, such as locks don't work, then its time to figure out why that bit doesn't work.
An LS most likely has a higher V (check the voltage in your new car vs an old one) output alternator. If you haven't changed/fixed the wiring in the old truck, you most likely have connection and ground trouble.
Alternators are typically rated in Amps, meaning Amps at X voltage, but the load is typically less than what the alt can produce due to resistive connections limiting current.

In short, you can connect it to Hoover Dam, at the right reduction and rectification, but the load (wiring, switching, etc.) is the trouble.