My strategy is going to be to lay out both harnesses and keep any wires that will continue to be used; ie: non-engine related. Those wires that will be needed from the WRX harness will be merged into my current harness to replace the unused wires from the previous engine.
In your case, serious, it may be beneficial to you to pull both harnesses and then start with the WRX harness and merge in any wires that are NOT engine related. Basically, the direct opposite of what I am shooting for.
I dunno, it could go either way.