2003 Mazda B2300 Rough Idle/Running below 2,500 RPM

A couple weeks ago, I was on my way to work and as I was coming off the interstate during the commute, my truck started idling really rough and feels like a misfire. I changed the coil, plugs, and wires, but the truck continues to run rough.

I borrowed a buddy's car computer and it rang up some codes saying the O2 sensor was leaning out in bank 1 (2.3L) and then code P2004 for the intake manifold runner control being stuck open. I replaced the vacuum switching valve in the system that is typically what goes out in the system. Still a no go, and removed the intake to replace the actuator (at the rear of the intake connected by a vacuum line to the VSV). I reassembled the intake on the truck and verified everything was connected and hooked up correctly, and it still has this rough idle that feels like a really bad misfire. Runs fine once it hits 2300-2500rpm.

What else is wrong with my truck?