Have you left a couple of injector pipes loose so the air can get out of the pump?
Did you clamp a line when you removed the bowl? You say you refilled the bowl, are you sure you have got fuel to the top of filter.
Check you have fuel right to pump, manually pump with lift pump, make sure there is a good flow and you are not being fooled by fuel that was between filter and pump before you changed filter which is causing an air lock. Then leave an injector pipe loose, and crank her over. DONT crank too long and damage the starter!!!!
If no joy!!!!
I had an excavator that self bled after fuel filter change, then one day it was a PITA and had to be manually bled. I started having problems towards the end of shifts, low power etc, but next day machine was good as gold. This went on for a few days till she finally lost so much power I couldn't work !!!
Turned out the in tank filter on the pick up pipe was part blocked. As long as fuel tank was full, (start of shift ) everything was fine, good head of pressure. Once the tank got down the head pressure dropped and she struggled to get enough fuel.