Technically, a Holley manifold is ITBs, since there is no plenum to speak of.

For an EFI throttle body, I'm using a 750cfm carb (4x42mm throttle plates) modified for 1:1 secondary action. Worked awesome on a 4 port bridge port. I have it on a 6 port stockport and I can barely get it to idle down to 1100 or so. Would be easier with smaller throttle plates. It's a bit touchy on tip-in because of that, too.

I had been using two 1000cc injectors in the stock primary location. I'm using stock GSL-SE injectors right now for finer fuel control.
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i'm not entirely sure what you mean by "adapting the Megasquirt to the stock harness." it's a standalone, so you just wire it up according to the diagram, (hopefully) get it started and then tune for your particular setup. the Gen 2 cars are not CAN-BUS or anything like that. they don't need integration. as far as i know, the rest of the car will work just fine with the Megasquirt doing it's thing.

Sorry I should’ve been more specific. I found a adapter that allows the MS2 or MS3 to plug directly into the stock engine harness for the 13b. My plan was to use that and then modify the stock harness to work with the tps on the throttle bodies, and whatever other sensors I would need.

on an S4 the TPS uses a pretty basic 3 pin plug, it would be really easy to make your new TPS plug into it.

i have an FD engine and ECU in an FC and i made a couple little patch harnii for the different sensors.