[David]

I doubt the alternator is the problem. I assume the 40psi was the pump pressure and not the regulated pressure. 40psi would probably be about right for a cold engine. The CIS system runs richer with lower fuel pressure since lower pressure allows the fuel metering piston to open more. I would suspect a bad spark plug wire, bad ignition timing, or incorrect fuel pressure. The spark plug wire can be checked with an ohmmeter, the timing with a timing light, and fuel pressure with a CIS testing gauge. It woudn't hurt to check compression and engine vacuum also.