mhopton,
I can only comment on the airbox modification. I removed the seat, then pulled out the rubber snorkel, leaving in place the CDI module (aka black box).
Don't mess with the CDI module for it'll cost you ~$200. With the snorkel removed from the top of the air box (just pull it out, its only glued in), use a hack saw blade to enlarge the opening. I placed an old rag over the air cleaner to collect all the plastic pieces that were displaced during the sawing operation.
This opening will allow the engine to breathe better. While I was at it I also installed a breather kit onto the top cover of the engine. Stroker Speed makes a lot of after market stuff for improving the TTR 250. This breather kit replaced the rubber hose from the valve cover to the bottom of the air box.
This breather kit was a rubber hose with a K & N air filter on the other end. This kit reduced the potential for back pressure within the engine (~$35).
As far as the carb, well I replaced it with a Mikuni 33mm from Stroker (~$350ish). Improved overall performance by ~ 30% (seat of the pants observation). Recently, I had to switch back to the stock carb, the Mikuni was acting up. Stock carb looses a little when compaired to the Mikuni, and has a noticable "pop" when off rev'ed. Even with all the mods I installed, I didn't perform any adjustments to the stock carb (like re-jetting, clip adjust).
The first thing I did to my TTR was remove and replace the exhaust system (boat anchor). Replaced it with a Stroker unit (~$200) dropped ~ 4lbs and improved performance, not to mention a better sound (more 250F-ish).
good luck,
fergy