Um... Just what is happening?
The guy asked you to change his output transformer? Was the old one defective? Or did he want a "better" one? In which case he was HOPING for a better sound, ie different sound. But now he DOESN'T want a new one because it will change the tone? What am I missing?
I am guessing you did not get an actual fender Prosonic output transformer and are instead using some sort of aftermarket type?
If you replace a transformer with a different brand, they may use different color wires. So you may have to change the wiring colors, but the plate lerads still go to the tube plates, the 4,8,and 16 ohm taps would wire to the same places. etc.
I genuinely have no idea why you would need to change a filter cap to replace a transformer. WHy would that be needed? Perhaps if you posted or linked us to that data sheet...
I don't "upgrade" parts for no reason. I do it with a specific goal in mind. What specific issues would you want to address in the amp by changing parts?