I know you 'think' that you have a new fuel filter, but replace it anyway. Disconnect the lines and blow them out. Then hook it all back up and see if the problem persists, if so, it very well could be the pump.
One way to see if its the TFI module is to get it running and then pull the SPOUT connector just distal to the TFI module, if it continues to run and evens out, then the TFI is bad. If it continues to do the same thing, then you likely have a fuel pump/accumulator problem and I would start by rexamining the way you have the accumulator plumbed.
You could try removing the accumulator altogether and see if that helps as well...but you did say that it was running fine before, right? I would try these things before I start dropping coin on parts.
FWIW, I am running the Carter 4070 with a section of hose to my E2000 pump for ~18 months and 16K miles without issue (due to the pumps or plumbing anyway). I had an obstruction(s) in the fuel pick/filter last year, that gave exactly the symptoms you describe. Hence, the comment about double checking the filter and lines. Just remember the KISS principle; it ridiculous sometimes how simple and stupid (it is or you are or both).