After 5mins or so I can't get above 3000 rpms, please help.

It starts up fine, runs like a brand new truck for a
few minutes, then starts struggling. When it's
struggling it won't go over 3000 RPM, when i try to
force it over 3000 it'll start getting misfires. If I'm
really easy on the gas and creep my RPMS up
slowly I can usually get it higher then 3000. I just
dropped a new engine in because of a spun
bearing, but I had the RPM problem with the old
engine too and am afraid to screw up this new one.
The only parts of the old engine that I kept were
the intake manifold and the vortec heads, recently
replaced the injectors and fuel pressure regulator
because I had 2 leaking poppits. Runs better but
still have the RPM problem. Ran straight pipes
thinking it might be a clogged cat but still no
progress. Distributer is timed correctly, timing
chain is lined up correctly. I'm out of ideas. Please
help, thank you.