What year bits are you using? This is important to know.
The only KLR600 rotor that I have on hand is an '84, and that is useless to glean information from because it was a one-year-only rotor, not compatible with electric start, and the reluctor bar was clocked completely differently.
Here are the Gen 1 ('87-'07) and Gen 2 ('08+) rotors. The photos show the relative placing of the reluctor bar.
This is the Gen 1:
This is the Gen 2:
If you can look at the rotor that you have, perhaps you can modify it to mimic the reluctor that is on the KLR600 rotor that you had in place. The KLR600 reluctor was long and interrupted. The Gen 2 reluctor is long and continuos. The problem is that I don't know how long the KLR600 was, in terms of crankshaft degrees.
There was a guy in Mexico who modified a rotor by welding a pad on it. I was aghast, as welding usually has bad effects on magnets, but he said it worked and the charging system didn't seem affected.
I know this is not a great deal of help, but where do you think you can go from here?