I had an L not long back, put like 13,000 Baja cruise miles on it, loved it! (and miss it)
I removed all the smog stuff with (as i recall) a kit from IMS. I can't say if it ran differently because I never rode it with that stuff on.
A good source for info on that bike is Thumpertalk.com, in the 650 R/L section.
Don't go overboard on bike mods, it really doesn't need much to be totally fun. I had Precision Concepts do the suspension, and IMS tank, different bar mounts (to get the bars farther forward and higher, and I'm only 5'8"), decent bars, and i monkied with the stock exhaust tip.
The IMS kit will not affect how the bike runs. If anything you might get a little better throttle response. You will also drop about 4 pounds of weight. Here is a link to some other mods you can do to enhance your bike. http://dirtrodders.com/xr650l/specs.html