Don't know if this old story will help at all?, but back in 1976 I bought a brand new Yamaha RD400 trail bike - I got someone from work to give me a lift at dinner time to the dealer to collect it, and rode it back to work. By the time I got back to work it was running a little rough, but I presumed it was just because it was new, so carried on working. When we finished work I couldn't start the bike - it just kicked back (it was a 400cc single cylinder two stroke), and it was like someone hitting the sole of your foot with a hammer -
REALLY painful. So I stuck the bike in the garage at work, and made my way home somehow?.
The dealer was closed by this time, so I rang them first thing the next morning, and they arranged for someone to come out - and they were coming about 1:00pm. So a little while before 1:00 I got the bike out of the garage ready for them, and one of my workmates Paul asked what was wrong with it - so I explained the problem, and offered him a try to start it (knowing that it was seriously painful
). Anyway, he kicks it and it started - so I went a quick ride round and it was working fine. I'd just got back and the guy from the dealer turned up, with an empty bike trailer on the back of his car.
So he came across and asked what the problem was, so I said it won't start - sat on a running bike - so he took it for a ride and came back saying he couldn't find anything wrong with it, so to try it again and see how it goes. He got off the bike and walked towards his car, and I got on the bike and it stalled when I tried to set off - he turned round and looked at me, and you could read from his body language what he was thinking
I tried to restart it, and it was kicking back again - so he came across and tried himself - needless to say it wouldn't start, and by the time he'd finished he could hardly walk. So he put it on the trailer, and took it away.
As they were unable to repair it with in a couple of days they lend me a bike, and when I went to collect it, I noticed that every member of staff was limping? - perhaps no coincidence I thought?.
Anyway - back to the reason for this long story.
They replace the CDI unit, and it didn't cure it - and eventually Yamaha themselves sent an engineer out, and he replaced the coils under the flywheel - this cured the problem. Later on the same year, while still under warranty, the same thing happened again - this time the dealer fixed it themselves, but never actually mentioned what had been done to cure it.
I ran the bike for a few years, never had any more problems with it, then sold it to a friend when I bought a car - he in turn sold it to another of our friends, and I eventually bought it back and ran it a further few years. However, both of my friends who had it replaced the CDI unit at least once - but again, I had no issues while I had it. I eventually sold it to another friend, who in fact I now work with - I'm not sure who he sold it to.
So issues could be the CDI unit, or the coils, or both - but there's nothing you can do without both of them working correctly.
I presume you can't just buy new parts at a reasonable cost?.