FORKS
Several people have told me that the biggest difference you can make to your XR650L is to put a fork brace on the bike. It will greatly improve the tractability of the bike over rough terrain, and I've heard that even on the road the steering becomes much more predictable. The most popular fork brace out there is the Summers Racing fork brace. I haven't tried one yet, though.
The XR650L's forks are really decent forks. They're 1987 CR250 forks, which have a reputation of being one of the most dialed set of stock forks you could buy off the showroom floor in motocross history. But the XRL weighs nearly 120 pounds more than a CR250, and you'll find that when you hit the trail hard, you'll bottom the stock fork quite a bit. If you do, first try increasing your compression damping. If that doesn't work, you can put a couple pounds of air in the forks, or try raising your fork oil levels. Look at Pro-Action's web site to educate yourself about suspension tuning.
When I did some serious trail riding with the stock setup (with the compression damping turned all the way up) I was bottoming on the smallest of jumps and even large braking bumps and dips. It was getting to the point of being very unsafe, so I forked out the money to have them set up by professionals. I sent my forks to Pro-Action to have them re-valved, cleaned and put heavier springs in. The difference was quite amazing and they work almost perfectly for me now. I weigh about 180 pounds and ride very aggressively, so if you find that your forks are giving you trouble, you might want to consider having them set up by a well-known suspension service.
SHOCK
Like the forks, the shock on the XR650L is a decent shock, at least in comparison to some other Dual Sport bikes out there, maybe only outdone by the smaller-displacement DRZ and expensive KTMs. Refer to Pro-Action's site to get info on tuning the shock. Make sure your sag is set properly before you hit the trail, otherwise you could be seriously endangering yourself. Spend a little time learning to adjust your shock in very small increments, you'll thank yourself as you start to ride more aggressively.
Here's a brief overview of how to set up your rear shock:
Lowering the bike
The XR650L is a very tall bike. For us shorter riders, its height can be a big problem. Whether it's simply getting a leg over the bike when there's gear strapped to the rear fender or when you're putting your foot down on an uneven trail, it's sometimed terrifying to realize you can't find the ground. White Brothers makes a lowering kit for the bike that entails quite a bit of work to install. You'll need to install a bumper on the shock that prevents the rear wheel from swinging too high when the suspension bottoms, and you may want to lower your forks as well. I haven't done either of these modifications becuase I want to keep the maximum amount of suspension travel I can. Anyone who has, feel free to write me and I'll tell all there.