So I just paid off my used 2006 GS500 with a little over 5000 miles, and of course, that would be when I am having problems. I went to start it up about a month ago and it wouldn't start and made a clicking/knocking noise. My grandpa deduced it to being spark plugs. So we replaced the plugs. In the process we found the crumbling fuel line, and replaced that as well. We wanted to replace the spark wire as well, but were told that it cannot be replaced by itself, so it was replaced with a car spark wire (compression wire). Now the bike starts, but if it is doing anything under 4000 RPM, it sounds very throaty and continually sounds like it is backfiring. And before anyone suggests it, yes there is gas in there. Any help would be greatly appreciated.

Did you charge the battery before starting it? The click click is usually the starter relay.

No offence to Grandpa, but I think the spark plugs are a red herring.

Per ke7syv's reply, did you or gramps recharge your battery at any point in this process?  A weak battery could have enough juice to activate the relay, but not enough to turn the starter.  That would account for both the clicking and the nonstarting you initially encountered.

Is it possible that you disturbed something while trying to get it started?  I'm thinking about that crumbling fuel line you eventually replaced.  Pieces of that may have partially clogged the jets in your carbs.  Since the problem only presents itself at 4000 rpm or below, I'd look very closely at your pilot and mid jets.

'06+crumbling fuel line? That doesn't sound like anything you would expect from a 2 year old bike...just sayin 

Quote from: Suzuki Stevo on January 05, 2009, 09:24:41 PM
'06+crumbling fuel line? That doesn't sound like anything you would expect from a 2 year old bike...just sayin 

I had an 05 and had to replace the fuel lines from the tank to the petcock for the same reason, cheap cheap fuel line. 

By compression wire do you mean supression wire?  Auto plug wires have long had resistance type carbon cores that were used mostly to supress spark intereference with the radio, not really suitable for motorcycle use.  You need copper core wires like came on your bike.

The GS500 plug wires are bonded into the coils and are not really removable and are sold as a unit with coil and wire being one piece.  I would never change them unless they came loose in the coil as one did on my 02 GS.  I replaced it with a piece of this wire, put a big dab of diaelectric grease on the end of it before screwing it into the coil:

http://www.denniskirk.com/jsp/product_catalog/Product.jsp?skuId=2021&store=Main&catId=412&productId=p2021&leafCatId=41209&mmyId=

Crumbling fuel line?  I don't believe it.  Put 80,000 miles on my 97 GS and have over 66,000 miles on my 02 GS and never had a problem with the oem fuel lines.  They have a mesh cover on them to keep them from wearing thru if they are rubbing on the frame and/or engine and that mesh cover gets frayed on the ends and looks worn but that means nothing. 

If your bike sits a while and becomes hard to start you can jump it from a car to start it (car not running while jumping) and ride it to charge it up and it should be good to go after that.  At 5k miles you aren't even due for your first plug change yet.

gsJack aka greatgrandpaJack but my great grandkids call me Biker. 

I'm going to assume that the original "click click" was from a dead battery, except for the fact that it had been ridden not 20 minutes before. I guess I forgot to mention that when we replaced the fuel line, we made sure to flush everything out as well... And yes, I checked, it's a suppression wire. Would a new wire make that much of a difference?

A new wire is not required unless the old one is really bad. I'm sure theres a specified range the resistance of the wire should fall in to. ie. 1.8-2.6 ohms or whatever.
The three things required are spark, compression, and fuel/air. If all three are present and your timing isn't way off, it'll start. Check for signs of fuel after cranking by removing spark plugs and smelling for gas as one would do to determine if the engine was flooded. You should be able to check for spark by holding the spark plug's electrode about a 1/4" away from the engine and looking for a spark between the gap. It should be blueish not yellow or orange. For compression use a compression gauge. The battery doesn't get much charge under 2500 RPM so if you had it running but kept it at idle the battery was powering a percent of the system. Hope this helps.