It does sound like you cleared it up...but, then again, the moment I say that...
The big yellow wires? On a fuel injection engine I'm not sure...the only yellow wires my 88 had were in the ignition connection for the starter circuit...the 96 had about five yellow wires but they were all merged and came out the firewall a different colour...I never bothered to TS them because the engine (2.3) was running when I tore it down and the wire harness was transferred into my 88 along with the entire dash and steering column.
I imagine the Haynes manual would list what they are and mine is just outside my door currently so I can look and maybe send you a pic later...dang hot out there right now and doesn't look like we are going to get any reprieve from it today.
I was just reading another thread about the fuel line check valve on the two pump systems. There is (or was) a fuel reservoir in line with your fuel pump from the tank and it is kind of odd shaped...that is what the other member was having problems with that caused rough running but also poor starts because the fuel pressure would not come up properly.
If this persists it might be something worth looking into though...as it prevents proper pressurization of the fuel and, therefore, running/starting issues...
I know your truck seems to start fine (most times) so I didn't think this was relevant to your issue.
Keep us informed either way if you have time...always good to hear something is finally fixed...