valve float/hesitation

well i put my skunk2 intake manifold on my 2000 civic si. after doing so i noticed a knock from the engine, the engine has to crank a few times now to start, and when i am at about 3-4 thousand rpm cruising sometimes it feels as though the rpms kick down about 500rpm for no reason. could these all be caused by a valve problem? too much air and not enough fuel? not enough fuel pressure? broken or leaking vacuum hose? any ideas please!