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I had this same problem on my 97. All details were the same minus the security system obviously. I have a push button on my starter and the bike would fire up that way but not by the starter switch. Problem wound up being a broken wire in my handlebars coming from the start switch. And no, I had not done anything with my handlebars in the past two years.
With everything you checked I think it is either your start switch or a broken wire either in your bars or under the tank somewhere.
I ruled out loose starter bolts, handlebar Run/Stop switch and the ignition switch when I was troublshooting the no turn over/no start condition.
I think the problem will eventually return as I didn't really do anything to fix it. I did change the start relay, but it will start now with either the new or old relay in it.
I'm pretty sure its going to be a broken wire to the start switch on the handlebar switch or a bad interconnect harness conection. I don't know how to check these if its not in a failed state. I am going to apply some dielectric grease to the fuses and relays. I'll also apply it to the harness connectors if I take the fairing cap off to further troubleshoot this.
I'm trying to decide if I want to chrome out the fork lowers and wheels via wiley shiney exchange http://www.willyshiny.com/ABOUT.html this would be a good time to get to the harness connectors for continuity checks. I have ordered this switch from dennis kirk so I don't get stranded somewhere if/when this no turn over/no start gremlin decided to visit again. https://www.denniskirk.com/201901.sku
If your sure you have ohms passing through starter switch. You might have a BCM (Body control module)On your 08 that might be worth looking into. Check all Grounds. Some times it the dumb stuff that it so easily over looked
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