96 Yamaha G16 lithium conversion wiring question

[robert@willcoteam.com]

I am in the process of converting my 96 Yamaha G16 to lithium. There are a couple of wiring issues that I am trying to filter through. It looks like someone modified a couple of the yellow wires coming off the back of the F&R switch and spliced them together on the harness side. (2 Pictures attached). Does anyone know where these go or come from. It ran fine previously and everything seemed to work fine.
Also, when I convert the batteries over to lithium, there are two wires attached to the + and - terminal of the existing charging port (Picture attached with arrow showing wires) that I will be abandoning. Should I just connect them to the + and - of the lithium ? Any info would be appreciated.