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Don't do the dynojet, it requires you to drill the carbs.  Just get bigger oem mikuni jets.  Buddha, a mod here, sells them.  You're not going to see much gain on the GS unless you start making serious engine modifications, maybe 3-5 hp.  In my opinion, the biggest reason for doing the can/lunchbox is so the bike sounds more like a bike and less like a sewing machine.

The GS500/E/F has about 40 rear wheel HP, always has and always will.  With a good job of jetting and with intake and exhaust modifications you can get another 10% that will carry thru to near redline and not drop off after 9000 rpm like stock GSs do.  Back in 89 when the GS was brand new Vance & Hines reworked one and included a 555 cc Wiseco big bore kit and porting work as well as their V & H exhaust and intake mods and only claimed a gain of 10%.

Annie's (co-founder of this forum) yellow GS had a good exhaust, intake, and jet reworking and the curves are linked @ gstwins.com, lt's a good example of what you'll get:

http://img.photobucket.com/albums/v443/jcp8832/AnniesGS500dynoRun-1.jpg

Typical stock GS curves look like this:

http://img.photobucket.com/albums/v443/jcp8832/MikesGS500dynoRuns-1.jpg

You may gain 10% up top, that is true, a 4hp max Yea. However you'd gain much of that from 2500 on. @ 2500 where you were making 10 hp or less, a rejet will give you say 2 more, @5K where it was 25 before, you may make 29. 2 in 10 is a huge advantage.
Also the bike will lose a lot of the ripples in the torque curve, that means better driveability @ all rpm's. Driveability is a lot different than outright power. If you think about it, an old vw beetle made barely 40hp. However driving one of those you never feel like it will stall. yes its not going to keep up with your friends mustang sure, but it wont stall, cough or feel like it wont make it. If jetted right and the whole thing is in good shape.

The stock GS is rather anaemic from the factory to clear emissions. They run emissions test @3k in first gear if I remember. They jetted the canada bikes better, a lot better than the US ones. I'd seriously jet a stock bike to the canada specs (40/125). Pipe and what not is what you like, noise and a wee bit of extra breathing. I actually prefer the stock filter, makes it last much longer.

Cool.
Buddha.

I am from canada and glad to hear that last bit abotu our bikes being jetted better.
I'll probably just leave the intake alone, get and exhaust and get the bike jetted to match. I was also told they are corked up real good form the factory. Mostly makes a differnce in down low if you rejet. They run real lean from the factory.

I think even if I don;t get an exhaust I'll get the bike jetted.