Jetting's as easy as 1, 2, 3. If the pipe didn't come with instructions. you could call the manuf. for recommendations. You usually go leaner with aftermarket pipes. This is what I came up with ; The following works quite well on my 96 KDX: B8ES, Belray 50:1 with Sunoco 94 octane, 152 main, 45 pilot, center clip on stock needle, 1 1/4 out on air screw, Pro Circuit plat. pipe, P.C. Spark Arrester, 12/47 Talon sprockets, Regina Gold O-Ring, M78 Bridgestone. The only reason I change the plug is out of guilt from leaving it in so long. Never foul plugs, even on the slowest, sandiest trails.
When I added the Pro Circuit pipe I went from a 160 stock main to a 158 to a 155 to a 152 main jet and from a 48 pilot to a 45. The stock jetting with the PC pipe made the bike loose power everywhere. If you're not sure what to do, talk to a shop or someone you ride with. Jetting should be as much a part of maintenance as changing plugs or oil.