its definately worth looking at your fuel return lines and also all unions and connectors. i had a similar problem for months on my old 2.25N/A i eventually gave up on it and parked it up, only to find out after that one of the banjo unions for the return had cracked, introducing air into the system
i know that its after your fuel filter change, and seemingly should have been happening before if that was the problem. but once there is a little air in i found that it helped the system introduce much more air in than when the crack was there and there was no air in. so it would definately be worth checking all your injection return lines and unions, i would also reccomend cracking off the injection lines at the injector with it running to bleed that last little bit, can make all the difference (sorry if i am telling you how to suck eggs)