As mentioned by Tom Schmitz above, Danielsand, and shown in the wiring diagram, the clutch/sidestand/neutral safety switch logic must be fulfilled (or defeated) for your bike to start. Otherwise, the starter circuit relay will not activate, and the starter relay (misnomer: "solenoid," a name for a neo-obsolete relay-cum-mechanical-starter-engagement-mechanism) cannot close and thus cannot send power to the starter motor. Reckon you COULD bypass the starter circuit relay, rendering it, "normally closed." Comments, anyone?
As to safety switch logic, the neutral switch wire runs perilously close to the countershaft sprocket; bears watching.
The Generation 1 (NOT Generation 2) engine kill mechanism is grounding the stator exciter coils' connection to the CDI unit, with either ENGINE STOP or IGNITION switch, as shown on the wiring diagram. Thus, any short-circuit (or open circuit) of this connection prevents engine running.
Now, NOT an electrical issue: Since you've read extensively of the KLR, Danielsand, you're doubtless aware Generation 1 KLRs remain particularly vulnerable to DOOHICKEY failure, possibly resulting in catastrophic collateral damage. Don't know if you've discussed your doohickey yet on the forum; unless the part is already upgraded (preferably with Eagle Mike lever and torsion spring, though lower-cost options exist), might be a good idea to perform the mod. Plenty of how-to videos exist, and some inmate will gladly loan you the special tools for the task without charge, should you desire to make the change. Kawasaki recommends a new rotor bolt when replacing the rotor, but the decision whether to re-use the original fastener remains yours.