I did something similar a few years ago, I used part of my 99 truck harness in my 97 truck harness in a v6 to v8 swap. I left all my emissions stuff in there tho, and now those plugs don’t go to anything under the hood, but they are there, but I never had any problems like you’re describing. I’m wondering why you had to combine harnesses to get lights and things, that I don’t understand ? All you got with the engine was the stuff connected to it or why did you have to merge two harnesses ?