Before this last "episode" I attempted the procedure listed above for turning it over 2 or 3 times then going till the decompression lever clicked, then let the kick lever up to top and then gave it the almighty startup kick. It backfired every single time I did that, so I quit it. Up till this it didn't backfire at all since the last bad one and it was starting reliable 1 or 2 kicks, just had that constant stumble/miss. Also the last time it did this I had just filled up with super unleade 91octane, then by draining and switching to 87 from another station, it started up again. I was running on that gas all the while till I filled up again with 91super, but at the same station that I got the 87 from.It wouldn't start after that. It couldn't possibly be that it HATES 91 octane (no ethanol), and will only run on 87(with ethanol)???? I do know the bike is running rich, black sooty plug, but I put in an iradium plug the morning before.
Is there any chance the regulator could cause the miss, due to it not missing for the first minute, then the miss starts. Also when I rode to work at 40F, it ran better(less missing/stumbling) than when the temp was warmer later in the day. Something was staying cooler and allowing it to run better.
The rich running condition wouldn't cause that much missing could it? Smaller pilot? lower the needle in the primary carb? Out of sinc carbs? It ran great under acceleration!

I'm pretty clueless with the "black box" technology of CDIs etc, but the heat issue does point that way, as per earlier posts in here - the usual advice is to obtain a replacement part and do a one-for-one swop, but I guess these things for your year are quite rare nowadays.
Buying one is the obvious way, but swopping out, temporarily, with a buddies bike is an alternative.
The prices you mentioned earlier are in the same ball park as those asked in the UK, if that is of any consolation.

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Dave

I know how frustrating it gets... Again, with a DR600, if I failed to kick it first try - forget it, it won't start (or it will backfire badly). Even warm/hot it was a misery to kickstart it. Always jumping on the kick lever as if I'm willing to break it, or as you say, bury my foot 2 feet into the ground. But it ran really good once started!

Get a manual, check the pickup coil for resistance, if it meets specifications, then CDI if it meets specs. Something is wrong with it, and it's no miracle... Find a good (bike) electrician, maybe he could shed some light on it.

I've heard of electronic bike/car components that used to function too early when warmed up. It might be the case there too.

Good luck!
Tadas.

Well I got the replacement parts that broke from the kickstarter backfiring. I see that when it does this I am still pushing on the kicklever and it prevents the starter cogs from disengaging and it slams into the stop plate, thus shearing the bolts(which are not made anymore).
I got a low mile cdi online to swap out plus drained the 91octane premium gas and put some 87 back in. I took the chance and decided to start it and concentrated on "the procedure". It fired up in 2 kicks and ran same as usual, purred great for a minute then started to miss, but not nearly as much. I did turn up the idle speed and that helps.

The local Yamaha dealer told me in all the years working on these and other Yamaha's, the number 1 failure electrical part is the pulse pick-up, by a big margin to the next part =cdi. So I am looking for a new stator/pulse generator for the bike.(I don't care to buy this one used). I've seen several companies that offered some but they all are different from each other so I have to do some calling to find which one is the correct one.