AIRBOX- the air box on most bikes can be one of the easiest and cheapest mod you can do on your bike. First thing you can do is rip out the snorkel. Simply remove the seat and then on top of the air box is the snorkel just pull it right out. The snorkel is not there to keep water out but rather to keep sound in. On my DR the snorkel opening was about the size of my pinky. Some people will just drill holes in the side of the air box but I think that would be a risky move unless you plan on never getting it wet. After pulling the snorkel out will have to re-jet the carb.
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CARB- one word…. Qwiksilver, Edelbrock's Qwiksilver carb is the best out there. Jetting is made easy, no more mid air stall outs or G-stalls. Adds about 5 more house power that you can feel. This is a must buy!!!!!!!!!!!!
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EXHAUST- At one time I loved my FMF exhaust but because I can no longer get the mega max II for my DR, I was forced to go with suppertrap and I must say that the move has been good.
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BIGBORE- can we say more power! If you are like me and you ride a thumper, a 350 is weak and it must have more power moremoremoremoremoremoremoremore. That's why I sent my bike to thumper racing where they did a 435 over bore can we say power!!! Be care full when you do an over bore because most of the time you will lose reliability.
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JETTING- I hate jetting, but if you have a Qwiksilver carb you would not have this problem. On the bottom of this page is an another page that explains jetting.
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GEARING- gearing is easy and fun. I like to leave the counter sprocket alone, changing this sprocket will have more of affect on the bike then the rear sprocket. The lager the rear sprocket the more torque you get but you also lose top speed. Now the totally opposite is true for the counter sprocket. Renthal web page explains gearing far more in-depth it's worth taking a look.