A hop up project needs to be a well thought out combination of modifications that compliment each other. You can't change just one thing and expect good results. You also need to have an objective. You need to plan for the rpm range you want to engine to produce it's best power in, how that will affect what it's installed in, etc.

If you modify the exhaust, yes, then you should modify the transfers and intake accordingly. You also have to plan your compression ratio, carburetion, exhaust, etc. One thing always affects another in an engine, and making single modifications rarely gives the results one is looking for from the engine. Research two stroke hop up techniques before making mods that may ruin the engine, or at the least provide poor performance.

Good luck and have fun,
AV8TOR