Ok so I looked at the diagrams again, the relay setups are different.
here is the STi:
here is the Baja:
So it appears that the Sti is setup for dual speeds where the baja is a single speed for individual fans. This poses a problem I think because when the ecu is telling the fans to run "low" it is only having fan relay 1 triggered, and then on high it triggers relay 2 and I assume turns off 1. But the baja needs both 1 and 2 to be on simultaneously to run both fans I think at a single speed.
I am running a Sti ecu with sti fans but baja turbo wiring. I know people who have run sti ecu's on their baja turbos so maybe the solution is to get baja turbo fans but I don't think the fan itself is different, as the plugs are identical so I theoretically should already be doing that.
Can anyone tell me what to do here? I don't get what the switch is between pins 30 and 33 on the baja diagram are doing?
Just tonight I swapped the Sti A/C compressor out with my legacy one, so they are interchangeable for anyone wondering in the future.
I also feel like my intercooler is sitting up too high that it will hit the hood if it's fully closed and I rev the engine/drive. In looking at baja turbos with STi TMIC's they seem to sit lower so I'm wondering if they have different intercooler supports that are a bit lower or if the throttle body is in a different location(which I doubt).