Air box mods

I have just recently purchased a 2002 XR650R setup as a motard with 17" wheels and the only engine modifications being an aftermarket exhaust and smog-pump block off kit. Has anyone tried the XR's Only High flow side panel modification Kit? Or The XR's Only High Flow side panel kit? $24.95 vs $124.95. Don't really want to spend the extra $100 unless that side panel is really worth it. Is there something better? Also wondering if anyone has tried the "Honda's 49 state intake manifold" for those of us who purchased from CA. Just trying to get it to run the way it should. Any other suggestions? I don't know if it has been rejetted or not yet.

You will need to do the full unrestricting kit, as doing just the airbox mod alone will give you no benefit.

First, put in the 49 state free flow intake manifold, take out the airbox block offs, and rejet the carb, with both the main and needle jets.
Second, put in a Uni style air filter.

If you really want to be able to utilize airbox mod, you will need more than just that.

You will need FULL exhaust, meaning header and exahust.
After that, you can do the airbox mod, and you will need to rejet again. Follow jetting guides as posted on this site.

As for an answer to your original question, the difference between the cover and the cover mod is more or less an appearance issue. Where the cover mod you cut 2 holes in your cover, and rivet an aluminum surround and mesh over the cover, the cover you can buy has many small holes drilled into the side. Depends on which look you want, as they both deliver pretty much the same performance.