Sorry, I'm having trouble reading my screen so I missed part of your post.
I don't have any practical experience on this, but from some of the posts I've read, I think he might need to get one of those PCMs he has flashed for the conversion.
One thing you can do is use the search function near the top of your screen and start typing in some search engines on the subject of PCMs for engine swaps.
Another thing you could do is call a facility that repairs & flashes PCMs & see what they have to say. This is absolutely not a plug, but I did have my PCM repaired by a place called SIA Electronics in Tilden, Il. If you do a google on them you will probably get a phone number you could call & inquire.
There are undoubtedly other places as well. That is just the one place I have dealt with.