I recently swapped out my handlebars and reran the internal wiring. I ended up having to use waterproof connectors to connect all the handlebar wired to the harnesses. Now after a while of riding I get a check engine light and then the battery light and red dot on speedometer come on. Once this happens my speedometer and light cut out then come back on. What is going on and how can I fix it?

 

Fine...

 

Year and model?
Did you disconnect the battery first?
Canbus wiring is not like serial bus wiring.
Obviously you did something wrong when you wired the bars. Pinched wire, loose connection, etc. Go back over it and check every wire and connection carefully. Use a DVM to check continuity.