P0305 code

I have a 96 explorer with a 4.0l 4x4. I've been replacing a lot of parts to pass our state inspection and unfortunately, more problems have been creeping in as I fix others. I started with P0401, p0305, p0171 and sometimes p0113 and p0174. I replaced the plugs and wires, the DPFE sensor, cleaned the MAF, replaced the vacuum lines to the DPFE sensor due to some cracking and installed a wire tie on the IAT connection because the clip had broken off and replaced the fuel filter. At the same time I installed new inner tie rods and upper control arm on the passenger side and shackles on the leaf springs. I cleared the codes and took it for a test drive of about a half mile, when I returned and parked in the driveway, the water pump started leaking. I replaced the pump, topped off the coolant and warmed it up with no issues. Took it for a 45 min drive to return the fan clutch tool and a p0171 showed up, but ran fine otherwise. When my girlfriend took it to work, it started misfiring and blowing smoke. It now has codes p0304 p0305 p0306 p0171 and p0174. I know what obd2 says they mean, misfires on 4 5 & 6 and lean on banks 1 & 2. But does anyone know where I can start to fix them?
When I got to her work to take a look, I didn't see anything obviously disconnected like vacuum lines or plug wires. The alternator seems to a little noisier than I recall from earlier today and there's a puf-puf-puf (best imitation of a exhaust? Leak) coming from the passenger side.