[Richard]

Just two generic comments. Not trying to be a smart alec. Take a hard hard look at what you changed. If the new separator is leaking air into it , or any of the touched fittings is leaking then it would cause what you are experiencing. I am sure you have rechecked the install, but wouldnt hurt to look again.

Second thought is to put your aux priming pump into the system temporarily. Run the inlet from the tank instead of a fuel can