No cover. Not yet. I'll probably rig one up just in case. Rode 2 hours straight in a driving rain storm last Summer, didn't hurt it but I stayed moving so it wasn't like dumping a pitcher of water right into it. Yeah, Biketronics or similar unit will give you use of your stock hand controls.
2012 CVO RGC/Renegade Lincoln Phantom 21-17/RWD Fender/-2 Mono Front -1 Burly Rear/Bad Dad Side Covers/Andrews 54H Cams/HQ Black Ops Lifters/Heavy Breather/Cometic .030 HG/Barnett +1 Clutch/Aim 480lb Spring/ClutchWiz/Hayden M6/D&D Fat Cat 2-1 w/UPB & Ghost Pipe/TTS MasterTune 2/Wiz's Tune/Alpine CDE-HD149BT Head Unit/Alpine PDX-M6 Amp/Hertz HCX 690/Hertz HSK 165 XL/Biketronics Module/Cycles Sounds Lids