I had a horribly warped L6 header (about 3/8" end to end) straightened by a local machine shop with very good results, and only a $40 bill. They used a large press to take away the majority of the curvature, then ground the flange to ensure it was flat. If you go this route, just make sure the final ground height of the flange matches your intake! Otherwise, you'll have trouble getting a good seal using the factory intake / exhaust washers.
First off, great project! What was the process/cleaners/paint used to restore the Webers and manifold? Also, what undercoating did you use? Sorry for so many questions..just awesome results in both cases! Thanks Casey
Might want to add the fan clutch to the list...from my research its designed to stay engaged until 2500rpm or so when it disengages. Upon deceleration it will reengage at approx 1600rpm where you seem to be hearing the noises. Heres a link with more detail: http://www.hammondsplains.com/newtechtips/cooling/index.htm The fact that you can hear the noise at the fuel pump, and its location near the water pump, leads me to the fan....hope this helps! Beautiful Z's by the way, I've spent many hours (maybe too many) looking at them! Casey