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I'm probably wildly off base as I'm not sure your bike (or bikes in general) even HAS one, but it sounds like a problem with the ignition coil. You're clearly getting a spark, just not enough of one. As you plugs, wires, and gapping all seem to be correct, and the rotor appears to work, it's the first thing that comes to mind for me. Granted, this is from a guy who knows cage mechanics mostly, but it may help. Not enough voltage hitting your plugs would cause a weak spark as you've mentioned, and outside having a half-dead battery, a faulty ignition coil would provide a weak spark at best.

Good luck getting her to run, I've got some tuning myself to accomplish in the near future....glad I found this site :idea:
 

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Check these things:
1. check resistance on the spark plug caps. They unscrew from the wires, use your meter to check resistance THROUGH the caps, if its more than 10 ohms its junk.
2. while you got the caps off, check for corrosion inside the plug wires, if they look a little green snip some off and screw those caps back on.
3. check for ac output at the pulse generator. I think you may be a little confused on how this works.. Its not like a car where the rotor distributes spark, its a magnetic pulse generator (transistorized ignition). All that rotor does is pass through a magnetic field, telling the computer its time to spark. Check for AC output like this: Set your meter on the AC scale and unplug the wires from the pickups (theres TWO 1&4, 2&3) Connect your meter leads to p/u coil 1&2 and crank the engine, you should see some ac current maybe 8-15 volts. Repeat this test for 2&3.
4. If you havent already... test the ignition coils for resistance both primary and secondary.
5. Remember that there is no guaranteed check for the CDI box. Its a process of elimination, check everything else twice. If its all good... then its time to buy a new box.
 

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There's allready excellent advice in the replies, I'd like to put in some more.

The Kat's electrical system is very vulnerable to moisture, be sure the drainage of the spark-plug recesses is'nt blocked.
93er huh? well, you can be sure the sealing of the caps is gone, look at them, they don't seal the spark-plug hole very well now dod they?

I remember I made a rain deflector out of alu plate which blocked the gap in front of the spark-plugs.

She also stood me up once, it prooved to be corroded connectors under the right side fairing the part that's under your butt.
check all the connectors, and treat them with contact spray.

also use non-restistor sparkplugs, your baby really needs those with it's vulnearable electrical leads/connectors, so take the same plugs but then without the "R" you could even try the hotter version, with the & in the type designation.

Performance wise:
Biggest gain would be of course the engine swap, using its fathers (GSXR 750 RR pre-watercooled models) intestines.
or complete engine.

Cheapest solution would be the shorter gearing, yes I know, i't wouldn't get you more power, but it sure feels like it !
 
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