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I did electronics for a long time. Nowadays, most electronic devices have protection circuitry to keep the expensive parts safe. With motorcycles, the rider is the computer, so you can think of the protection switches as the same. Unfortunately, they use relays and switches. At least 90% of ALL electronics failures are the things that move: switches, relays, and knobs. Most of the rest of the failures are active components--- things that produce heat. On a bike, there are not many things that make heat--- maybe the R&R, or lights. If you break it all down, there are maybe 3 circuits on a bike: ignition, lights and signals, and the horn. To make the bike run, you can ignore the lights and the horn. You can even disconnect them while working on it. If you've completely changed the wiring, you can keep it simple. There are chopper wiring plans, even harnesses, you can search for if you want to do away with the safety switches. Personally, I'd rather just bypass the switches, but I'm lazy. I rewired a '72 Triumph once--- no safety switches at all, but still a PITA. Once you've isolated the ignition circuitry, it's just a matter of making sure you've got spark. Start with a fully charged battery, charged off the bike. Troubleshooting anything is the art of cutting it in two, and seeing which one works. If it won't crank, your starter relay or starter are likely bad, assuming your voltage isn't dropping at the battery. It can go down to maybe 11 volts, but below that there's a problem with having enough juice to operate the ignition module. If the volts drop too far, there's a problem with either the stator output or the battery itself. Stators CAN fail, but it's more likely one of the wires to the R&R. If it's still not getting spark, the ignition module might have failed. If you can see output from the module to the coil and have no spark, the coil might be bad, or the spark plug wire could be open. Once you have spark, and it doesn't run, you likely have a fuel issue.
One thing to remember. If you worked on it and it got worse, you did something wrong, so go back and double check what you did. Also, you said it's gotten worse over the time you've had it. How many miles on it? Does it blow smoke or use oil? You said it had been ridden hard. Have you checked compression? It's hard to wear out Japanese engines, but it can be done.
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