How to perform a compression test using a harbor freight compression tester 

Turning the motor over via the starter relay bypasses the need to keep going in and out if the cab. It also bypasses the fuel pump from being activated.

Your compression gauge may be wrong. I've had 2 harbor freight ones neither one read right.

Do a dry and wet test, wet test add a little bit of oil into the cylinder to seal microscopic leaks.

Do I need to disconnect the fuel? Wouldn't the fuel melt/clog the catalytic converters?

You need to stop the fuel delivery before compression testing. I pull the fuel pump fuse while the car is running and let it die before doing any compression testing. Replace the fuel pump fuse when you're done testing.