When were the spark plugs last replaced? I bought a truck straight from auction with a P0301. It would idle rough at stop lights and stuff. Put a new batch of plugs in, now the truck runs like it just rolled off Arlington Assembly.
Those fuel pressures are within spec. I know some stuff says 58 pounds running, and it should not run that much under no-load-pre-start charge (60psi), but 44 ain't bad. Fuel pumps either work, or they don't.
The 69 (hehe) code is related to manifold pressure, and 641 has to do with a few grouped sensors that try to read a variable. This would be three wire sensors, sensors that would tell the PCM how much pressure, how much temperature, etc, not like a binary or on/off sensor that would tell the PCM a condition is met. Knowing that, and knowing 641 is coupled with P0069, I would look at the MAP sensor to start, things that tell the PCM whats going on in the manifold, MAF sensors, intake gaskets, air filter. ****** like that.
The key to troubleshooting is to start small and eliminate the easiest, cheapest, and simplest part of the system thats giving you the problem. Work from the bottom up, not the top down.