Hey Matt ...
I too just did this install the other day and ran into the same issues & questions. Justin wrote back and told me that it's normal for our AC clutch to cycle the fan on and off as often as we're experiencing. And although I trust the guys on here that have done this mod, and Justin's experience, it does seem crazy, not to mention loud, to have them cycling on and off two to three times a minute.
Also, I have not been able to verify the blue 42 pin activating the drivers side fan like the LS1 directions instructed. I'm not all that anxious to undo everything again, but Justin said we could verify by grounding out the blue pin to get the fan to turn on.
Hope that helps and adds a little piece of mind. If you find/learn anything more of different, please post it here so we can all learn. I have to say, I was super surprised that the fan is as loud as it is, draws as much power, and cycles as often as it does.