[A1971Blazer]

Interesting issue, I'm running the same setup 2002 LS1 and Vintage Air unit.
I'm in the final stages of plumbing, but I haven't yet completed the AC install so I can't speak directly to your problem.

What I did, after consulting a friend that does lots of LS swaps, is to wire the ground from the trinary switch to the blue relay trigger wire from the PCM so that it will engage the primary fan either at the programmed temp or at the request of the trinary switch.

This is how my friend says that he wires them.
I'm not sure that it could back feed to the PCM since it's just a ground?