CAPS system. Just put in a Re-newed 8.3 Cummins in a MX285. Used old pump (it has only 8-900 hours since being replaced). Some days it will run 3 or 4 hours before acting up. After a few hours use it starts to de-rate. Shut off, restart and runs good for several minutes then does it again. Very sporadic, runs for hours at a time then starts throwing fits. Seems that when it is cold it runs better. Throws code # 329 which is CAPS pump has an overpumping failure. Even though it says overpumping what it means is it is starving for fuel. Changed filters. Checked the inline filter when I had it off and didn't get any algae or junk out of it like I'd been told I could. LIft pump is strong, pumps out a stream of fuel 1/2 inch diameter 2 feet from tractor. Dealer now thinks I have an obstruction in the tank. Wants me to take off and clean. 
Question 1. Anyone ran into this before and what did you do?
Question 2. I have had tanks off these before and I don't recall any way to get it cleaned out other than wash everything out through the fill cap. Is there something I'm missing?