1953 new Yorker 5.7 hemi 545 upgrade

Welcome to the camp.
I don't know anything about Swap Secialties. Don't they have any customer support? Seems they owe you some answers.
As already mentioned, Hotwire has been making these Hemis work for over 10 years.
You might consider changing to the Holley Sniper stand alone system.
You should post a separate thread here on FABO in the new Hemi Swap section.
There is a Facebook G3 Hemi group with a lot of smart people. Same thing, post your symptoms and they'll help you.

No offense, but I've been reading stories like this for 10 years. I went with the Chrysler wiring kit becsuse it's just about plug and play and I don't want to go through this. It works on passenger car engines 2013 and newer. You can buy the components separately too. (Unlocked ECU, wire looms, etc.) It does not support transmission control though. There is a guy in the Facebook group that has standalone transmission controls figured out. I think he goes by New German Engineering.
Good luck.