I purchased my 2nd GS500, a 2001. The problem is, I can't get it started! It sounds like it is misfiring when trying to start. Tried everything - cleaning carbs, new battery, new oil, new sparkplugs, valves adjusted, etc. Compression is 145 on both cylinders. The gas tank is spotless. When I was checking the valve clearances, I noticed that the signal rotor looks different from my 1995 (sold that a few years back). Low and behold, the signal rotor is for a 2004 or later model, with one large tab, and a number of smaller ones, instead of just one large tab.

Will the 2001 model run with a 2004 or later model signal rotor? I quizzed the previous owner, but he claims he didn't know that it was replaced (it had previous owners). I already tried buying a 2001 signal rotor, but the holding bolt for that rotor is too small for this crankshaft. That is weird, because the engine appears to be a 2001 model, with the 2 signal pickups, not 1, as on 2004 and later models. And the engine cases have the black suzuki plates, not plain aluminum as on 2004 and later ones.

What do you guys think? (And yes, I'm a dummy for buying the bike without seeing it run first.)

I can imagine a careless mechanic might strip out the rotor bolt while doing an inappropriate rotor swap.

Perhaps whoever is responsible for the "upgrade" also drilled out and re-tapped the hole.

Can you just reuse the bolt that was in there?

Seems like too obvious of a question, I must not understand what the problem is.  Can you post photos?

I think you could use that new rotor if you also had the updated single sensor plus the CDI that attaches to that sensor.  I've never seen it done before but it seems plausible.

Parts fiches show all years 89-09 GSs use same 6x60 size bolt holding rotor on so yours must have been drilled out by a previous owner for the larger bolt.  If they haven't changed the CDI or wiring perhaps a 01 type rotor drilled out for the larger bolt would fix it.   

Good idea and thanks!... I will get a used pre-2004 rotor and have it drilled out to fit the larger bolt. Will let you know if that cures the starting problem. Over to EBay....

I wonder if the DPO had possibly changed to a new cdi. Seems a lot of effort to tap a Crank when not required.
Might be worth checking before proceeding as gsjack suggests.
Are you getting spark on both sides?

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Yep...Spark for both plugs, although it looked a bit weak. The part I can't figure out is that the bike has 30K (km) on it, but the engine and side cases seem like new. Even the 4 bolts holding the exhaust on the cylinder head came out easily (no penetrant needed) and not a speck of rust on them! And the exhaust pipe itself had only a tiny area of rust.

Well, I got my used pre-2004 rotor (from a 1994), installed it, and bingo, the motorcycle started immediately and ran OK without stalling (haven't taken it on the road yet). Memo to file: 2004 and later rotors do not work on pre-2004 GS500's!
But I'm not out of the woods yet. The previous owner who installed the wrong rotor also monkeyed around with the key on the crankshaft. The old one must have bent or broken off, so he had it welded it back on. It was a sloppy welding job because the signal rotor has some play (clockwise/counterclockwise) before tightening the bolt. Based on this, I don't want to run it more until I can confirm that the timing is correct and is not too advanced or retarded, before I tighten the bolt for good. 
The question then is, what is the best way to confirm that the timing is correct to make sure that the key on the crankshaft was welded on at the right spot. Should I align the rotor RT & LT marks and check that the notches in the camshaft are in the exact position they should be when adjusting the valves?

Rotor should be located by a pin sticking out of the end of the crankshaft into the rotor.  Key is for primary drive gear.

http://www.shspowersports.com/fiche_image_popup.asp?fveh=2102&section=92662&year=2001&make=SUZUKI&category=Motorcycles&dc=3378&name=CRANKSHAFT

With rotor on RT & LT marks the #1 arrow on the exhaust camshaft gear should point to cylinder head top finish as showh here:

Advance it as far as slop allows and tighten it down. People used to spend alot of money on those advancer kits, I think V&H made one. Sounds like you just got a free performance boost!

This is all extremely helpful - thanks. Off with the valve cover again...