It is all about trade offs. The crimp tools for the milspec connectors are about $200, and about $400 for the autosport connectors and that is something to consider. I have the tools since I do this all the time, so for me, I always use them because of the racing environment I work with. For someone who is going to do this one time, maybe the investment is not worth the cost. I would not use other connectors other than the milspec or autosport because the don't work well as Don found out, although, I might look into using the factory round connectors from a 996 depending on cost. They however, are big and bulky.

Running it through a grommet with a well shrink tubed harness is a fine choice and properly done will work for year. FWIW, my 89 turbo which was the first serious one I did in 96 was mounted under the passenger seat, was routed through a hole in the chassis next to the center tunnel, up over the torque tube an into the engine bay. That engine was out almost every year and it had its share of dirt, grease, oil, and fuel spilled on it. Never had an issue with it. Nowdays, I try to come through the firewall on top of the left frame rail and mount the ECU behind the driver on the rear seat base where your feet would go.

I would be more concerned with the construction of the harness protective shrink tube than whether or not a bulk head connector was used.

 

I put my ECU under the passenger seat, and routed the harness through the rear bulkhead, in the center, just above the cover over the shift coupler. I then ran it along the underside of the body, above the transmission, under the crossmember that the shocks mount to, and into the engine compartment near the center, between the rubber flap around the engine and the engine tin at that end of the engine. It turns out there's plenty of give to the rubber lip that it doesn't pinch the harness, yet the rubber seals nicely around it. The hole in the rear bulkhead was just big enough to fit the largest of the engine connectors -- it's not big enough to pass the ECU plug through. The hole is surrounded by a rubber grommet. You can get grommets of any size imagineable from Aircraft Spruce, if you're looking for a source. If I want to remove the engine, I unhook 13 connectors, which takes a couple minutes. If I want to remove the whole harness for any reason, I pull it through the bulkhead into the passenger compartment.

The point I made earlier is that if you're removing the engine to do something minor, like change a clutch or adjust the valves, then the bulkhead connector may save you a couple of minutes. But if you are taking the engine out for anything more major, like pulling the heads, then nothing is gained by having a bulkhead connector because you'll have to undo those 13 connectors anyway once the engine is out.

 

I just got back from the shop- there's really no way to run the wiring through the bulkhead a' la Geoffrey's setup and maintaining the rear seats due to the closeness of the rear seatbacks and their configuration. Since I'm not willing to remove those, it looks like we have to go with a connector and route the wiring through the side sill and out the panel in the left upper portion of the engine compartment.

 

Look just above the rear fuel pump. There is a thin rubber cover over a 1'' hole that will allow you to run wires through it. If you peel off the undercoating, you'll end up with the rubber cover. From the inside, it's just above the driver side rear seat floor board, next to the inside rocker. This might work for you?

 

I'll try it- thanks.