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You probably don't want to hear this, but I use custom, double insulated wires that are all the same length and route them on top of the valve covers, not under the ex. manifolds, so I will have the same intensity of spark and keep them cooler.
rg
i think over the top makes more sense for the tuner. keeps wire heat down which increase conductivity. also, less hassle and less likelihood of frying a plug wire on a manifold or header. my .02.
I routed my replacement plug wires back per original. Route the front wires STARTING at the spark plug and going BACKWARDS towards the distributor. This has you pushing the plug wires DOWN through the motor mounts. Pushing the wires down through the mounts is a piece of cake compared to pushing the plug boots up through the mounts.
In any case, routing the wires over the valve covers has got to be cooler but I liked the appearance of the stock motor (under the exhausts).
On the drivers side, I made a slight cut at the end of the wire way and routed the wires around the engine mount to the front two plugs.
The passenger side is a different story. I am going to do what mapman suggested. I plan on removing the boot for the distributor end, cut off the spark plug boot on the old wire, tape them together and push/pull the wire through the wire ways. It may be necessary to remove the start, but I hope not.