I did just what you're wanting to do. I run a one wire alt and MSD in my B body and I removed all the wires from the bulkhead connection on the engine side except for the temp and brake warning light and a switched 12V. The only other wiring is the forward harness for lights etc. I'm gonna put foam in the bulkhead connector to prevent moisture from getting in there. The wiring look so clean now.
Good luck!
P.S.
I did keep all that wiring I removed in case I ever want to go back to something stock.
