I realise that this thread is a few months old and the problem has probably been sorted but thought my experience with losing power on one cylinder might be helpful.
About a year ago, my 2005 Speedmaster started cutting out when warm and then died altogether - classic pickup coil problem (tested it and it was a goner). Replaced the pickup coil and it ran fine for maybe a week or two when the right hand cylinder began intermittently cutting out.
The problem didn't migrate to the other side when I switched around coils or cables so I bought a Procom igniter. Bike ran well most of the time but misfired badly when cold.
The misfire got worse until the right cylinder would no longer fire at all and, with winter and other matters that I had to deal with, the bike sat idle for several months.
Fast forward to last weekend, when I found some spare time. Took out the spark plugs and found one was very black (the one that had been in the misfiring cylinder) so gave them both a good clean and put them back in. Bike ran okay but had a misfire on one cylinder at low throttle openings and WOT. Put in a set of new plugs and it runs like new, doesn't even play up when cold, which can be a problem with Procom igniters.
I'm a bit disappointed (and embarrassed) that I missed out on several months of riding because of something as simple as a carboned-up spark plug but the moral of my story is that failures (especially electric ones) upstream can have consequences for components downstream and you should always check to see whether the downstream components (particularly cheap ones) have sustained any damage before deciding it's all too hard.
