Does anyone have any ideas...
1989 GS500E
I've been through a lot with this bike I have. 
Original issue.  The bike was making a clicking sound when trying to start it.  I thought it was the starter clutch.  It turned out to be something internal.  I purchased an engine from ebay.  The sorry engine I recieved is currently in the bike.  I was able to push start it but it wouldn't stay running.  I don't think I should run it for any length of time with out the rotor secured.
I've already swapped out an engine and it seems to have an issue with the bolt on the left side.  The bolt holding in the Rotor and starter cluth.  I can't seem to turn it in all the way.  I busted the bolt on the right side holding it while tightening the leftside.  (Note to slef: don't do that again!)
I fixed that situation then tried taking it ot the local power sports shop but they are backed up 4 weeks+ and require a $250 deposit just to look at it.  So it is up to me.  My son's bike is becoming a nightmare.  I've looked at the Cylmer book and I didn't see anything special about putting the left side back together.  I don't remember it being so difficult taking it apart!  *sigh*

The current engine seems to run but all I need to do is secure the bolt on the left side.  One problem is it seems the internal threads are damaged but I don't know for sure...

Anyone...? 

Wow. Where in SC are you?  The RH bolt just holds in the ignition timing rotor and should never be used for leverage -- as you found out.

I am having trouble believing the LH, rotor bolt, won't tighten up if the rotor is pressed properly onto the crankshaft. It screws directly into the crank shaft so if the threads are messed up there...BAD NEWS.

One way to keep the engine from turning over while tightening or loosening the LH rotor bolt is to put the bike in gear and use a padded bar or wooden bar through the rear wheel spokes. Let the engine rotate the drive chain until it clamps down the bar.

Of course if you have taken the chain off...that won't work.

Have you looked over my FAQ posting?  CLICK HERE to see it.

I also show some of the same invasive stuff on my webpage.

For the Engine Section CLICK HERE.

Its possible the thread in the crank may have stripped or be clogged with dried Loctite. I think the only option open to you is to run a Tap down the hole in an attempt to clean out the thread, unfortunately I dont know the size but if you take the bolt to a Engineers merchants they might be able to match it from the thread and supply a suitable item. You need a Plug Tap, its not tapered and will cut right to the bottom of the hole. Use some light oil when cutting and keep the Tap parallel with the axis of the crank, cut a quter to a half a turn at a time then turn it backwards to free the swarf. (There are plenty of websites that will explain the technique). I would use a brand new bolt too as its threads may now also be damaged and use Loctite or similar when refitting as the thread in the hole may now be weakened. Another tip for locking the engine when the covers are off is to place a copper coin between the primary gear and clutch basket. As you turn the engine over, it becomes jammed and locks the engine solid. It works in both directions so you can loosen or tighten bolts and because its far far softer than the hardened teeth of the gears it doesnt damage them in the slightest......but you wont get the coin in a slot machine afterwards  Best of luck.

Thanks for the ideas!  I like the coin option and the foam around the bar...I did the bar thing but had to pound it back out afterwards.  Since the bike is already marked and scraped up it doesn't matter all that much but knowing these other options will help when I get around to working on a more polished cycle.

I appreciate the confirmation about the threads.  I will look into the non-tappered tap but shouldn't I be able to just retap it with a normal mm tap?
It should be a 12mm or 13mm thread I can verify with a gage.  The Rotor threads are 14mm.

Thanks again ... I will need all the luck I can!

The hole may not have what you call a normal M12 thread. Its not just the diameter of the thread that is important, you also need to consider the pitch of the thread, this is the distance between the ridges. For example a threadform with a major diameter of 12mm can have one of 4 pitch options, 1 course and 3 fine. Look at the table in the link below which indicates thread data, go down the fist column and you will find 12x1, 12x1.25, 12x1.5. These are the 3 recognised sizes for metric-fine, the figures after the x indicate the distance in mm between the thread peaks and despite being the same diameter they are not interchangable. i.e you cant get a M12x1.0 bolt into a M12x1.25 hole and vice-versa. The 4th option is metric course, it has a pitch of 1.75mm and is always indicated as just M12, this generaly is the most common size but again is not interchangable with fines despite the same major diam`. Metric-fine threads are used extensively on japanese bikes and its possible the hole in the crank may have any of the 4 pitches. If trying to just clean out the thread you need to use the exact size tap, trying to retap to a different pitch will not work as it will just completely remove all the thread remanents and you will be left with just a 12mm dia blind hole. If the the thread cant be cleaned up it may be possible to bore the hole out and cut a 14mm thread but for it to be a successful and reliable repair the crank would have to be removed from the bike and the work done by a machine-shop at some cost. Note also there are no recognised threadforms with a major diameter of 13mm (but that doesnt mean to say they dont exist)
http://www.newmantools.com/tech/threadmf.htm