I have been looking towards the aftermarket for quite some time now, and have been having a hard time finding bolt-ons for more power. I have a K&N filter, but thats all. I would like to get a full exhaust system, then i can get a jet kit. Does anyone know what pipes are available for the Recon? I am just looking for a couple extra horsepower for a little better acceleration. also, does anyone know what all has been done to the 250ex? i know its a recon motor, but what gives it more power?

FMF and Supertrapp both make exhausts for the Recon. I don't know if the FMF uses the stock header pipe but the Supertrapp comes with a new one. Dynojet makes a stage 1 jet kit for the Recon it comes with 3 main jets and a new needle. K&N jet kit is a repackaged Dynojet kit, I know this because I just bought one. You can buy a complete hop up kit from Highlifter or you can save some cash (esp since you already have the K&N filter) and buy the exhaust and jet kit from somewhere else like Rocky Mountain ATV (which is what I did because I wanted a Uni filter instead of the K&N).
The 250ex has higher compression and I think it has a slightly different carb and valves but I may be incorrect about that.

I have a Recon with the Supertrapp on it and it fits/works great. I also cut the end of the airtube off so it gets more air but had to re-jet to a 110 because it leaned out so much. I think those jet kits are a waste of $$$ when you can buy single jets for around $3 but that's up to you.

I read somewhere that the 250EX has a different head design to inprove flow.

Hope this helps,
SMC