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You removed your intake and exhaust manifolds and valve covers... but you didn't bother to change the timing belt, water pump, etc? Also change the rear main seal while the engine is out.
This is a great time to flush the block too.
As for the wiring, you can reuse your KA lower harness so the part with the wires cut, where you describe it, shouldn't be critical. At least, where you describe it, I don't have anything branching off of my RB harness. Just my KA lower harness that I combined with the RB one.
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