My charger puts out 40.5 V. Is this normal?
It depends on the state of charge. If this is open circuit charger output, it is too low.
Trojan pack at 36 V is to equalize at 46.5 V. Is my charger faulty?
It likely is . The prime suspect would be the capacitor, and its associated wiring.
See pages 1-16 through 1-20 of the Homeowner's Service Manual for the most concise diagnostics. Follow them to the letter.