To start with it would be useful to know why both the membrane pad and the transformer were replaced. For example, transformer secondary open or transformer visibly burnt and membrane pad blank or non responsive etc. ? Obviously the replacement membrane pad would be OEM ( Original Equipment Manufactured [Pentair]). Was the transformer also OEM? What is the supply voltage that the heater is using? The OEM transformer is listed as using either 115V or 230V on the primary side. Was the new transformer wired correctly to the supply voltage? What were the original symptoms when the heater was not working? When you say the heater tries to run with no input from the membrane pad, I am assuming that you mean that the combustion blowers runs with no observable input from the pad? This should be the manual for your heater
https://images.inyopools.com/cloud/documents/pentair-heater-mastertemp.pdf The wiring diagram and ladder diagram are on pages 36 and37.