The PCM is adjusting the fuel pressure based upon input from the FRPS. For the PCM to "think" that the FP is 40 and assuming that the external gauge is accurate then the problem has to be in the FRPS.
Check the fuel rail pressure sensor intake vacuum reference line for raw gas. If any is found this means that the FRPS diaphragm has ruptured.
Ensure that the FRPS intake vacuum reference line is connected and leak free (likely it is in your case).
2003 GT Convertible (sold)
2000 GT coupe (fix up project)