Motorcycle Repair: 1998 flhtcui, crank sensor, o rings

Question
i just had the bike in the shop complete top end gasket job, new cam/crank sensor or whatever that sensor is behind the timing cover new 32448-95b 180 bucks had new o rings fuel injection , but the bike will idle up to 3,000 rpm after a bit drops back to norm pulled plugs both black when starting sounds like hitting on one cylinder cuts out when throttleing but sometimes runs perfect. im stumped..  

Answer
You could be running on one cylinder since the plugs are black. They are fouling. Fouling plugs dont fire well. I am not sure why you are fouling plugs since I cant check the work that the shop did, but I would take it back. Somthing they did is wrong.
Good luck and happy riding
Mike