Take a look at Diesel Giant's purge page and using this modified pop bottle, make a temporary fuel tank. This should eliminate the tank and lines to the pre-filter or where ever you plumbed.
If this modification worked, you have 1. bad fuel 2. something in the line or tank. 3. ?????
I have seen vegie crud build up inside a line 'on the wall' till it let loose making a flap valve.
If this temp. tank does not work, keep going up stream. Only after checking flow to all injectors and doing the above, would I look to the IP.
I believe IP's should fail slowly or over a long period of time.
I assume you did not find the wonderful black crud in the per-filter, have added biocide & have done a water test on your alt. fuel and verified the tank strainer.
? Did the vehicle run ok on this batch of fuel before the problem raised it's ugly head?
?Did you 'bleed' the fuel lines at the nozzles?
Good luck and please post the results.