Update - Put everything back to stock. Hoping that I had separate issues.

1. The fuel system was causing the drop in RPM. - Fixed after the cats were removed.
2. Removing the CATs and adding that aftermarket bypass caused the codes.
3. When putting the CATs back in I found that one of the manifold temp sensors was not connected and the other had a broken wire.

Testing tonight.

Yes. As soon as it started, "service engine soon" was flashing.

Does anyone know of a good cheap code reader I can buy to erase the codes?

At this point you need to buy the scan tool (you really should have one if you're going to own a computer controlled marine engine).

https://www.rinda.com/rindashop/?sfi...tic-converters