Firstly, you need a decent set of headers and as a bare minimum, a fairly free flowing 2.5" header back exhaust with mandrel bends and a high flow cat. If the engine can't breathe, don't expect it to make any power/torque.
Secondly, did you remove the Swirl Control Valves in the lower half of the intake manifold?
Third, if not, did you correctly hook up all your vacuum lines and ensure that you don't have any vacuum leaks?
And Col is right, get an antrx chip for your ecu; the stock chip runs notoriously rich in the top end which will kill your top end power. Noss's chips fix this and improve driveability greatly.