Thanks for the quick responses and warm welcomes. I should have been more careful writing a topic late a night.
The 2005 bike that had the blown engine is a 2005 Rocket III Standard, it has what I believe is a neutral switch with a two pin connector right near the drive shaft at the back of the engine/transmission. The replacement engine is from a 2008 Rocket III Standard, it's neutral switch has a slightly different internal design and has a three pin connector. I assume I will need to splice the wiring somehow. The service manual I have from triumph doesn't specify wiring enough for me to figure it out. I will be uploading photos later tonight. Thanks for the help!