I just had to have a used engine (90k) installed in my 2005 v6. The mechanic said there was a misfire when they first started it up after installing the new engine so they changed the spark plugs. He Said that helped and then they let the truck run a bit and all seemed to clear up so he said it was good to go. After driving it a few hundred miles we noticed it idling a bit rough but not too bad. Tonight while in traffic the engine started idiling really rough, then it started sputtering a little and the check engine light blinked a few times. As soon as traffic picked up and I gave it some gas the check engine light went off and it ran fine. It's still idling a bit rough but is otherwise seems fine. Does anyone have any suggestions on what we should check first? We just bought this truck and immediately had to spend 2k Ina new (used) engine....we are so stressed about pouring any more money into it!

 

Did you get a compression test print out on the used engine?

I would read the codes in history, if CEL was on codes were stored, if it was flashing CEL then probably misfire codes, it would be helpful to know if it was a specific cylinder or random misfire.

Could just be a loose intake manifold, not uncommon on 4.0l
This causes a local vacuum leak that only effects near by cylinder(s), and only at idle.
This creates a Lean misfire and since unburned fuel exits cylinder O2 sees Rich so computer reduces fuel at injectors which makes for an even leaner mix, so more misfires

 

Thanks...no I didn't get a compression test print out. Ordered from LKQ and it was shipped direct to the shop.

Would an auto parts store be able to read the codes or does the CEL light have to be on at the time they scan it?

 

Yes, most auto parts stores will read codes free, CEL coming on even once means there is for sure at least on DTC code in memory, but computer sets codes all the time without turning on CEL, so you could have some history codes that may be helpful.

Another option is a Bluetooth reader
All new cars and trucks sold in North America since 1996 had to be OBDII(OBD2) compliant.
OBD = on-board diagnostics, pre-1996 is OBD or OBD1, 1996 and up OBDII

You can buy Bluetooth adapters(they are OBDII only) that plug into the OBDII connector under the dash, they get power from the connector.
You can then read codes or watch live data with engine running and while you drive on a smart phone or laptop, assuming they have Bluetooth, the live data can be helpful with problems

The adapter runs from $20-$90 and the "app" is usually free, but check first, sometimes the adapter is cheap and the "app" costs.
I don't know of any that are better or worse, just read reviews
It is not a bad investment since it works on any car or truck made after 1995

Google: obd II bluetooth