Is the ground strap on the back of the inlet manifold on and bolted to the manifold / good ground? this is the ground to the ecu.
Being a 99 what are you trying to communicate to it with? as not much will com with it, and you said pump was priming to my guess is it has power.
Other alternative is as Dan has suggested what Crank and Cam wheels have you used, are they from original engine?
Have you timed Crank wheel to the timing mark and not the arrow... also very easy mistake, seen it timed to arrow at 3oclock in this picture many many times.
Simon
Simon