Modifying an EX500

Good modifications:

1. The stock fork springs are really soft (might be better in the newer models). Progressive and Works make replacements. Replacing them is a hard job, and it's worth paying a shop to do it if you can afford to.
2. If the bike crashes on the right side, the brake pedal can punch through the engine cover. Rearsets cure this, and also (for me) make it a lot easier to straddle the bike without getting caught between the peg and the pedal.
3. Dropping the bike on either side can reportedly make the stock front turn signals punch through the fairing -- very expensive/difficult repair. A lot of EX riders replaced the stock front turn signals with the minimalist "bullet style" turn signals available in almost any bike store. It's an easy fix, looks good and might save your fairing some day. (On the other hand, another EX500 rider reported that when she made this change, drivers noticed her less and seemed more likely to turn in front of her. I haven't noticed this myself, but be aware!)
4. Telefix fork brace. Easy install, stiffens the front end under braking.
5. Steel brake lines. (I don't think these are necessary, but they don't hurt ...)
6. Adjustable brake and clutch levers from a late-model Ninja 500 (but you probably already have those).
7. My bike also has a Works rear shock, but only because the stock one wore out. Stock is fine 'til it wears out.

Bad modifications:

1. Independant K&N air filters. Makes it easier to work on the carburators, but it had better, because it also makes the bike run like crap so you'd better be ready to work on the carbs a lot to fix the jetting. Also it makes the bike really loud, and not a pretty sort of loud. Don't do it. The bike runs so well with the stock setup, and is nice and quiet.
2. Telefix clip-on bars. I got these thinking that I could lower the bike by sliding the triple clamp down. Surprisingly, it didn't affect handling in any way I could detect, but it didn't really help the seat height either, and the reach to the grips was much longer so I couldn't do low-speed tight turns any more since I couldn't reach the outside bar without shifting my weight way to the outside. Also (I only noticed this after I went back to stock bars) on the older EX500s, the mirrors are positioned so that they block the wind to the handgrips -- my hands stay a lot warmer with the bars in the stock position, and I seldom need to use my warm gloves. (Really, Kawi did an awesome job on the aerodynamics of the EX500.)
3. I tried changing the gearing with the front sprocket (which is extremely easy to replace; the rear is more of a pain) but I can't remember the details. I think I went one or two teeth smaller to get better acceleration, but decided later that that was silly and there was no point to it, and I'm fairly sure I went back to stock there too.
4. When I changed the airbox I switched to a dyno-jet carb rejetting kit, and spent a while trying various needle settings. They all sucked, no throttle response and no low end. (And it's a pain to rejet, those carbs are really hard to get back together once their apart, especially when the bike is warm, because there's a rubber vacuum diaphragm that expands and then won't fit in the seats. Unfortunately, to install the air filters I had hacksawed the airbox in half, and that wasn't fixable, so I had to put up with it for months until I finally found a used stock airbox (I wasn't making much money then so I didn't want to pay for a new one). I was SO happy when I got the carb and air filter back to stock -- it seemed so responsive, powerful and quiet!
5. Exhaust. I didn't change mine, but most of the EX500s I saw with non-stock exhausts were really loud and obnoxious, didn't run that well (rejetted badly), and they had to remove the centerstand. I guess they were a few pounds lighter, but it's not worth it.
6. Corbin seat: fine for tall riders, hard on shorter riders, and the stock seat is much more comfortable.

Other comments:

I considered a steering damper, since my one bad accident on the bike was a tankslapper, but steering dampers have other problems and I didn't want to carve up the fairing.

My bike used to regularly blow the gasket on the crossover pipe between the two exhaust headers (I went through about four of them in a few months) then it completely stopped and has been fine for many years. Maybe I hadn't been tightening the clamp enough, or maybe Kawi improved the gasket.

I have soft saddlebags which I got from a Kawi dealer, of all places, that fits perfectly and carries gobs of stuff when I need to.

It's dead reliable -- basically never gives any serious problems even if I ignore it for months (except for needing a battery recharge).

It should be a great sport tourer (tank range longer than almost any other sportbike, very stable at speed, great fairing, comfortable seat) except for one thing -- the engine is very buzzy and my hands buzz after more than about 100 miles. If I was going to tour on it, I'd experiment with bar end weights or fuzzy grips or something.

There's lots of information on the EX500 at the Sport-Twin Ninja 500/EX500 Page.