Drivetrain 99 Mustang GT clutch pedal 'catching'

Not what you want to hear (maybe) but did you check your TO brg sleeve on the transmission? If it has worn spots, it'll effect the clutch operation and is what you'd typically feel when depressing the clutch. Was the TO placed on the clutch fork correctly? Was the ball fork lubed and in good condition? I'm also assuming you have all correctly mated parts. One other area is the clutch cable and/or cam (by the pedal). If that hasn't been replaced I'd ditch that and get a good firewall adjuster type. This is NOT intended to bash you but give you some ideas or pointers on what to look for.