Engine power issue - what is the most probable cause?

Lately I've noticed that my car runs into some trouble at high RPMs. At first, it was just a slight hesitation to shift to the next gear when it was close to redline (about 5800 RPM). However, the problem has been getting worse. Today I was driving uphill on the freeway and needed to accelerate. The car downshifted to accelerate, but then it wouldn't go any faster past 4500 RPM or so. I was stuck at about 60 mph with the gas pedal fully depressed. Then my Service Engine light came on. I went to O'Reillys to have the codes checked. They said I had a random misfire code. I tested the acceleration a couple of times on the way home, and it had the same trouble of not getting much past 4500-5000 RPM, but not shifting up either. I suspect a possible impending fuel pump failure, but I'm also not having any of the other bad fuel pump indicators (hard to start, engine stall, lurches, etc.). I was reading online and found someone with a similar problem who ended up having a clogged catalytic converter, so too much exhaust backpressure could be causing it too. I just don't have the knowledge to figure it out.

More relevant info:
-I replaced the fuel filter about 1000 miles ago.
-Blew a gasket and had to replace the engine recently. It was replaced with a nearly identical engine out of a 2005 Pontiac with 85,000 miles. The mechanics replaced the spark plugs when they installed the new engine. I assume they hooked everything up right again, but the problem has only become worse.
-I checked the control wire on the throttle body, and it appears to be properly adjusted.
-Air filter looks clean.