Cat 3406c rough idle off and on

Hey guys. Just wanna get your input. I have a mechanical 3406c 3zj and last month it was idling and just started running rough. I finally had the time to check ####. I threw a clear hose on it by the fuel/ water separator and it had bubbles in it. So I just changed both fuel lines since I was there. Also new fuel and fuel water separator filters. Pumped up hand primer till hard. Started up fine. But still does the rough idle off and on. It’s a single tank with top mounted fittings. I was gonna try Transfer pump next but you think it could be the solid feed line going in the tank pulling fuel? It only runs rough to about 8-900 then she cleans up and pulls.

 

if your talking about the one at the back of the pump with a 90 number 4 line. I actually pulled that first thing and it’s clean. I am gonna put a pressure guage on it today check fuel pressure. Hand pump primes till can barely push it in.

 

Okay so when I push the hand pump in every I can hear what sounds like bits of air escaping somewhere. Sprayed everything down with soapy water but can’t see any bubbles. Sounds like from the back of the pump somewhere!!!? I’ll keep snooping.