This might be of help to you if you have a Bonneville/America/Scrambler etc with similar symptoms.My 2006 Speedy started running very rough during the week. Power was worse the more I rode it and it started backfiring alamingly. I did all the usual checks but couldnt rectify it this time. It was barely ridable and would only run on partial choke.
I took the bike to Andy at Herts Bikes in London Colney. After various checks, he diagnosed a faulty L/H ignition coil which was sparking intermittantly.
New coil fitted, bike runs like new now . My thanks to Andy.