How do the brakes feel without the engine running ? ( engine off or no vacuum assist)
With out power assist it’s easier to determine if there is still air in the system.
With out power assist the pedal will be rock hard and it will take a huge pedal effort to stop but the pedal will be firm.
The disk upgrade will not feel like modern brakes ..........the pedel feel and travel is different.
As for the manual transmission conflict ........think some of that is for modern drive train upgrades. The shifter linkage and rear trans cross member can be an issue.