From my experience, swapping a matched ECU and BCU frees you from having them synced. The mileage shown on your odometer will be whatever was higher, the BCU or your original odometer. I usually sell the ECU, BCU and instrument cluster as a package so mileage matches and there are no issues with the odometer flashing.

If you have SAI get a combo from an SAI equipped truck.

 

Definitely check if codes are popping up

How badly does it misfire though?

Did you do a water test on your cables?

Just remember that a BAD MAF sensor can send false information to the ECU and still got undetected (NO OBD CODES).

When that happens, the ECU tries to compensate for whatever readings the MAF is generating causing missfires, engine bogging, backfiring, etc...

I'm saying this because it happened to me and in a situation where your engine is running rough, it's hard to pickup relevant LIVE DATA from any reader to help diagnose the problem. All you see on the screen is values jumping up and down unsteadily as the engine is not stable.

You can get a MAF sensor for cheap on amazon for $35.

I know a lot of guys will tell you that they don't work, but it's most likely because it wasn't the problem to start with or they got really bad lucky on buying electronics that day. It will work.

 

Get us the codes, if any

 

I can't remember all the codes but it is misfiring on all even cylinders and is throwing a p1300 code and oxygen sensor codes
I have pretty much replaced everything already, maf sensor included.
I drove it through some pretty heavy water at the river, it ran fine until I got home parked it and let it sit for 2 hours then it started misfiring the misfire has got worse and worse probably due to the fuel mixture not being correct, I replaced plugs wires, mass air flow sensor, fuel pump which includes the fuel pressure regulator and filter,the camshaft sensor,both cool packs, and tested for spark on all cylinders, tested the compression on all cylinders, and finally pulled the exhaust at the manifold to make sure there wasn't a clogged.
I'm running out of ideas please help.