Ok, finally got the vaccums taken care of, now a new issue... When you lay into the pedal to open the secondaries, you get a sputter, like not enough fuel. Im thinking trash in the lines, or fuel pump. Anyone have this issue before? Any ideas would help.

 

Is this weber new or used? To me it sounds like its jetted wrong for your engine... this usually happens from 2000-2200 rpm when it jumps onto the main circuit.
But Might be like you said about junk in the fuel and crap keeps clogging the jets. Its easy to check the jets in the carbs for dirt.

If your running the stock mech pump just make sure you run a fuel pressure Reg. after the pump to keep the pulses and pressure under 3.5psi. Ive been tweeking with my 38 for months now with jetting and float levels but it still is better than any stocker ive ran.