I can help with that. As it happens, I have nearly the same bike.
Start with a 30mm Mikuni, like you've indicated. Like this:
http://www.ebay.com/itm/30MM-MIKUNI-CARBURETOR-CRF-XR-100-200-250-CARB-ATV-CA09-/140749566922?pt=Motorcycles_Parts_Accessories&hash =item20c553f3ca&vxp=mtr Jets are cheap and plentiful for the 30mm Mikuni. Start with a 25 slow jet and a 110 main.
The stock airbox is fine, and you can use bulk Uni foam as a filter material:
http://www.ebay.com/itm/UNI-FILTER-BULK-FOAM-/360814108503?pt=Motors_ATV_Parts_Accessories&hash= item5402325f57&vxp=mtr I use Maxima Fab1 filter spray oil, which is available at most motorcycle shops.
If you want to try a pod filter, it's hard to beat this one:
http://www.ebay.com/itm/42mm-SPONGE-AIR-FILTER-FIT-PIT-BIKES-DIRT-BIKES-/321315058942?pt=Motors_ATV_Parts_Accessories&hash= item4acfdeb4fe&vxp=mtr Again, Maxima Fab1.
I'm not sure what performance exhausts exist that will bolt on, but it would likely be easy to install an FMF universal muffler:
http://www.ebay.com/itm/FMF-TurbineCore-2-Universal-2-Stroke-Spark-Arrestor-SILENCER-1-1-4-020303-/330966285652?pt=Motorcycles_Parts_Accessories&hash =item4d0f20bd54&vxp=mtr It's designed as a two-stroke muffler, but that doesn't matter. You can pack it with four stroke packing if you wish. I would.
That's a good start. If you perform these mods, your bike will wake up a little, but it will never be a freeway flyer. If you want a bigger cylinder and piston, that stuff is cheap as well.