Here is an excellent write-up by InvisiBill on the old Ninja 250(88-07) also Ninja 500 suspension by a fellow forum member on ex500, and Ninette. On theses bikes a lot people are going with a new newgen (08&up)250/300 rear shock. It's a cheap, effective way to get a much better shock.
I've done quite a bit of research and played around with a few different options on my 500, but definitely listen to the guys here who actually have real-world experience on these bikes.
Getting the spring right for your weight will allow the bike to bounce the proper amount. That allows the damping to have the best control over that movement. If your spring is too soft, it will bounce around too much and your damping system will have to work harder to try to constrain that extra movement. If the spring is too stiff, it won't compress enough to absorb bumps, and the wheel will skip.
http://www.ex-500.com/wiki/index.php...ension_Preload is a long read, but it has tons of info, and I think it does a good job explaining everything with examples.
According to RT's calculator, the rear spring is ideal for someone who weighs 220lb (100kg). People here have said that may not be exactly right, but the spring is definitely quite stiff compared to the other little Ninjas (it's 73% stiffer than the 500 spring). I'm assuming you're lighter than that, so going to a softer spring should make the rear work better for you. The PreGen's spring is good for about 140lb on a NewGen, but the shock is a little shorter so it would lower the rear and make the handling a bit slower (plus it lacks any preload adjustment). If you can find a decent one cheap on eBay, it might be worth tossing one in just to try it out though (they're usually ~$20 here).
The stock shocks are simple, non-adjustable, non-rebuildable, lowest-bidder units. Aftermarket shocks give you more adjustment options for tweaking the damping system (usually separate for compression and rebound) and are built with higher quality, replaceable parts (so when something wears out on it, you just replace that one part instead of buying a whole new shock). £395 is US$615 which seems somewhat expensive to me. A new Penske is about $800 here, and used ones can be half that. The nice thing about buying a new shock is that they generally include a spring and calibration to match your weight. It should be basically a perfect drop-in upgrade.
If you can do a bit of mod work, the GSX-R shock swap is a pretty cheap way to get a decent shock, and there are a variety of spring rates used on the various models (there's a chart of different rates/weights toward the end of the thread). It's not made specifically for the Ninja's suspension, and requires a bit of work to make it fit, but they're usually on eBay for about 1/10 the cost of that Brook shock. The SV650 shock doesn't have all the adjustments (it's comparable to our stock shock) but should require less work to install, as another cheap DIY option that's probably more suited to your weight.
NewGen Fork Spring Rate Chart
Again, the NewGen has the stiffest fork springs of the little Ninjas. It's still a tad low, but should be acceptable if you're smaller. If you're a fatty like me, it's still quite a ways off, but it is possible for it to match up fairly well to the weight of a smaller adult (unlike the PreGen and 500, which have essentially useless fork springs).
The stock front and rear are pretty mismatched, so if you're smaller and go with a lighter rear spring, you're actually reducing that mismatch and making it less-bad than stock. On the PreGen and 500, replacing a soft rear spring with something appropriate can exacerbate the problems of the super-soft fork springs (because you're increasing the mismatch).
If some of the links don't work,etc me know.