Jeep Strokers

I recently joined the stroker crowd and swapped my 4.0 for a 4.6 Titan in my 01' Tj. Was having fuel issues due to stock injectors and finally switched to 24# Ford injectors. Noticed that I started having stalling and misfires along with starting problems, all symptoms of a faulty ecm. I just ordered a reman 4.0 ecm programmed to my vin from car computer exchange. The ecm is plug and play but I'm expecting there to be issues because of the programmed ecm will think it's running a 4.0 instead of the 4.6 stroker. Is there any break in methods or tuner/flashpaq one could purchase to get this thing running smoother or will the new ecm be just fine the way it is?
Thanks

Hey I couldn't respond to your PM as somethings wrong with my PM outbox...

I am running a Stock ECU with 26lbs injectors with my 4.7 Stroker so if the injectors are correct size for your recipe then you should be fine, it will not be prefect but it should be good enough...

I am a 98 OBDII so I am not 100% sure about the 00-06 ECU's...
There are a Few Guys here Tuning Jeep ECU's which will know best But I think the ONLY Flash you can use for a custom tune is the SCT3200 flash however discontinued but I spoke with them and the New model SCT4 was not compatible at that time with the Older Jeeps so I am not sure what they are using to flash the ECU...

I think I am going to go with the split second controller for mine when my custom supercharger goes on which allows you to tune it from a laptop and not have expensive software to buy but I am just starting to look into that route as My engine has been running good so far with the Stock tune but I know I will need to do something once the Supercharger goes on..

Saw I had a pm on this. Never check this sight much, so appoligies on the delay. I have no answers, and for that matter the stroker is still patiently waiting in the garage to be installed. I have looked at possible options for ecm tuning, but no decisions on what to use if the stock ecm is not adaptive enough.

The ECM is adaptive enough. The crap leak-prone stock injectors that shoot liquid fuel to the combustion chambers are not. The ECM doesn't care about engine size. All it cares about is the crank and cam positions, firing order and at what duty % to fire the injectors based on feedback from the engine temp sensor and oxygen sensors. I had issues with a yard Cherokee ECM that used a body module/alarm and it took me a while to figure out why it would shut off so fast. When I got an ECM for a 97 Cherokee, the issue went away but my distributor timing was off by one tooth, causing it to start up with a really high lean idle and then chuffing to a complete stop after a few seconds. Remember, the computer controls air:fuel and some ignition timing but the initial timing needs to be right.