Correction: Compressing the gasket doesn't affect push rod gap. If anything, it moves the pedal a small amount. The gasket did compress from all the activity, so the nuts needed snugging up anyway.

I need to pull the MC from the booster and extend the push rod to close the gap to ~.020.
However, the instructions clearly say not to remove the MC from the booster because it can ruin a seal inside. I'll ask The Ram Man about how to do it without potentially voiding the warranty. As long as vacuum isn't applied to the booster with the MC off, it should be OK.
Thanks for your help.