Brakes locking up.

Jacmifish said

When I was taking the master cylinder on and off the mounting studs I noticed the piston is actually compressing when I put the master cylinder on (I can see the fluid swirl).

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THIS IS YOUR PROBLEM. The master piston is not returning far enough. The piston MUST return ALL the way back

You may have

wrong / incompatible master

Something wrong with booster, assembled wrong

Problems under the dash with that end, linkage, return, pushrod, etc.