I think the way you are changing your numbers is causing this issue.
Set up your PE to like 35-40% throttle.
If you are changing the Commanded AFR, you need to zero out the other AFR adders. Make the add vs rpm to 0 across the whole thing, make the AFR correction base table to zero, then set up how much timing you want to run while WOT. This how I do and it works fine for me.
Make sure you have all the correct injector data in the PCM, seeing how you did a top swap you must have had to switch injectors.
