think of it this way, with the 2 into 1 pipe set up you have, its like inhaleing through your nose and exhaleing through a single tiny straw, put 2 straws in your mouth and you can exhale alot easier. so ditch the 2 into 1 IMHO.
youll want to keep the airbox if your doing GNCC because of the mud, so drill holes in the lid and get rid of the snorkle.
22" on the rear is the only way to go. id have a few sets of sprockets on hand. some for acceleration and some for top speed, if you know the coarse is all turns then gear down in the front, if its straits then gear up in the front.
youll need a good strong chain, i recomend D.I.D gold chain, theyre strong and ive ran them on all my bikes, i never had to buy a new chain not even on my yz490. just keep it oiled and dont let it get too loose and keep an inch of free travel while you sit on your bike
id keep your stock carbs or maby get some 28's, (you can bore stock carbs to 28 for cheap)
also get things such as anti vibration steering stem, works suspension, etc. to give you more comfort.