So you bought a new RIC harness for $65+shipping, then added your own output jack, then spent 5 hours working on the wiring. Meanwhile, I build mono harnesses with the vintage tone option for 4001/3's for $100 shipped. In spite of the lame pot values, I'm sure the factory harness was built correctly, but with all the extra cheap vinyl insulated wire in the harness, you can't really tell where everything is supposed to go unless you already know how the bass is wired. You should be able to look at the pic I supplied to build a harness from scratch, but there are a few tricks that come from having built 100's of these that make it go together easier and last longer.
So maybe give that a double check before you give up. YOU CAN DO IT!