I bought a 2006 Ford Ranger 3.0l V6 with 236,289 miles. I was told before purchasing that it would need new heads. It would run, but, it was rough. Did compression test once we got it home. Both dry and wet. Concluded the seller was honest. So I ordered the replacement heads and bolts from Allied Motor Parts. And got to work.
Everything went back together smoothly with all new gaskets, seals, and proper torquing. If it looked like it needed replacing, it's getting replaced. Seller had told me he had just replaced the coil, plugs and wires prior to selling it, thinking that was going to fix the issue. I put new Motorcraft plugs in anyway.
Then came the 1st crank. Doesn't start! Cycle ignition to make sure fuel system is primed and retry. Still no crank. Try coaxing with a little throttle, she fires! But running like I Crossed a couple plug wires. I verify correct firing order and plug connections. Check fuel pressure KOEO- 42psi and Oddly 50psi running. I verify spark with an in-line tester. Gets fire at all 6 cylinders. I triple check everything I pulled and reinstalled. Then check MAF (looks brand new) and IAC valve (dirty). I clean IAC valve and reinstall. Truck will now crank mostly on its own. Idle is still rough like it has a misfire. I've scanned and have No DTCs at this point. I let her idle for a couple minutes before noticing smoke coming off the passenger side (Bank 1?) Exhaust Manifold. Jump in and kill it just to be safe. Thinking that maybe it was just the penetrating oil I sprayed before disassembly burning off, I let it cool down.
The next time I crank the truck, I see the light! Finally, a clue! Pull the code, I get 2. And as I'm writing this I can't remember the numbers. One was intake temp sensor circuit high, the other was Idle Air control circuit high. Replace both with Motocraft replacements and clear the codes.
Truck now cranks and idles slightly smoother but there is definitely a misfire type feeling. Knowing everything I've checked and replaced, I pull out the good ole multimeter and check my injectors. I getv12-13 Ohms on each. So at least I know they should function.
I grab my IR Temp gun and crank the truck up. This is a cold start. Run for 60 secs exactly. Temp on passenger manifold is 425° while the driver side is only 170°. Some very colorful language when I think to myself. The passenger side cat must be bad, plugged, or at least restricted. Except soon realize as I crawl underneath, that 2 of 3 are missing. No, the local Metthew didn't strike, they're piped through. And it still has the big one that both downpipes run to. I decide, that even though I don't think it's the Cat now, I'm gonna disconnect it and at least verify. Other than the sound, No Change.
Okay, i think to myself, running back through everything. Maybe it is the injectors. With the engine running, I start pulling harness connectors loose, yes, one at a time, and listen. Cyl 1- truck stutters, Cyl 2- slightly less than 1, Cyl 3-6 definite stutter/ miss. I let the truck run just clear fuel out of cylinders. Then pull plugs. Only 1 didn't look ok for have all of 11 minutesof run time. Cyl 2 plug is still damp, smells of unburnt fuel, but does have carbon build-up like it fires.
With No codes to go off of and the extreme temperature difference on Ex manifolds, the only thing I can think of is fuel issue. With no way to test injectors at home, I decide to swap injectors. Bank 1 to bank 2 and vice versa. Cold crank, same issues of rough idle/ misfire. I let it run for 2 minutes exactly. Check temps on manifolds. Passenger manifold 483° Driver manifold 68°. Ambient Temp at time of test was 57° So my problem technically got worse.
I've researched the vastness of the interwebs, prayed to the entities that our ancestors did, begged God's forgiveness, thought about selling my soul, and now I've stumbled here! I desperate need of guidance. So anything will help.

RECAP: 06 Ford Ranger 3.0L V6
New Cylinder heads with new bolts, compression at 160psi +/- 2 psi across all cylinders
All new gaskets and seals
New coil, wires, and plugs. Spark and order verified
New Motorcraft MAF sensor
New Motorcraft Idle Air Control Valve
Fuel Pressure KOEO- 44psi Eng Running- 50psi
Cats checked (missing 2 on downpipes, piped through. 3rd at collector still installed)
NO DTCs
ISSUE(S):
Truck will crank. Rough idle/ misfire.
Extreme heat difference in exhaust. 2 minute run time. Passenger 483° Driver 68° Ambient 57° ( at time of test)
Swapped injectors to see if the issue moved but it only exacerbated the original problem.