The one wire without a plug is for Heated Grips.

Order a replacement TGS. About $100.

 

I posted the exact same question a couple weeks ago when I attempted my 10 inch bar install. All that was wrong with mine was when I rebuilt the six wire connecter from the throttle I got the wires mixed up ......twice.
It wasn't until I posted this on the forms that somebody sent me a picture of all the wiring should go and all was well. My throttle went wide open also but I cannot answer your issue of the gear mechanism not meshing with your grip. And yes I did my bar swap on my own after hearing how much our local dealer wanted to do a swap on my friends 16 Fatboy S, IIRC it was north of $2600 CDN.
So I guarantee that you have two or more of the wires in the throttle by wire connection mixed up or perhaps not making a complete connection with the other end..
I found that it was a very rewarding project. I am getting pretty bad at doing things in my old age but doing the handlebars and any exhaust work is quite fullfilling.

 

Also, double check the seat on the TBW assembly. It's keyed and should only go in one way. The grip and TBW may not be seated together all the way either.