04 R1150R battery replaced and now bike runs like garbage

Ran fine before battery died. Added a USB charger and trickle charger wire. Simple items. Now bike runs like shit, loud clutch rattle in neutral, and bike runs like the fueling is messed up. Yes, I reconnected the quick connects correctly (labled red and blue) and the two breather lines.

So basically I just replaced the battery, added two simple transparent items and bike is way off. Any ideas what could be causing this and hopefully a fix. The bike sat for about 10 days with the bad battery as I was out of town.

Any suggestions welcome