The XR650L is jetted very lean in stock form, and re-jetting is a good idea.
I replaced the stock filter with a Twin-Air foam alternative that I have used before, and not had problems with.
I replaced the whole exhaust system with a more free-flowing after-market setup.
I also removed the smog pump and charcoal canister.
All this allows the engine to breathe a lot easier, and as a result the already lean carburation is even leaner.
There are countless threads all over the internet on how to do this. You can buy larger jets individually, or as I did, you can buy a kit with replacement needle, spring and jets. I went for the 'Dyno-Jet Stage 1 Kit'
There is a tab on the mixture screw that hits a stop on the carb body and prevents you altering the mixture beyond a certain point. This can be ground off to make adjustment easier.
I went one step further and replaced the phillips head screws with socket cap heads.