There is nothing wrong with the fan wiring. I have been driving the car on different tunes for 3-4 years now.

I also have several modified Memcals so I could drive on one and burn to another. They contain SST 27SF512 chips.

I did semi figure out a couple things,

I copied the timing tables from an ARAP bin I downloaded from here. I pasted it to my stock AYPN. When I pasted it, some values turned red and were lower than what was copied.
I assume there is something else in the tune that would need to be changed to allow for the higher values?
I thought Scaler because I saw things like max advance. But that in both tunes were set the same.

I also noticed that when I went into the ARAR timing tables that the numbers were waaay different (much lower across the board) than the ARAP, APYN and a Hypertech tune for an 89 Camaro.
So as for the no start with ARAR, I think the ARAR tune found on this site has been modified. But I dont know where else to look for why the fan switch change does not allow the fans to NOT come on with the key on engine off.

I will try your ARAR bin.

Thanks