The best thing to do is to remove the entire harness before you put in the cage and work on it out of the car. It is MUCH easier to put in the cage without the harness, and much easier to work on the harness as well. Put the harness back in after the cage is in and painted. That makes everyone's job easier. Fab guys don't have to worry about melting the harness with welding, the painter will have almost nothing to mask and when it goes back together it is very straightforward. Installing a harness is no big deal. Working on a car working around a cage sucks, so do everything that you can out of the car!
When I do a harness, the only wires I cut are ones that go through the molded bulkhead grommets that will be removed. The only other exception is if components are moved and wires need to be shortened or lengthened. EVERYTHING comes apart. It is tedious, but the end result is what I think would have come out of Porsche Motorsport.
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'03 S, manual, 18" Carrera wheels, PSM, PSE, Litronic, 996 Cluster, +
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