The problem here is going to involve 1 or more of the following systems and or components . ( These are the most likely ) In no particular order they are ;
FUEL TANK SOCK .
FUEL INJECTION PRESSURE REGULATOR
FUEL INJECTORS
IGNITION SWITCH
IGNITION COMMAND MODULE
IGNITION IGNITER -if separate from last item .
IGNITION COIL/SHIELDING
IGNITION SPARK PLUG WIRES - this includes more than we are currently discussing here . Good to know : internal coil - no coil lead - if my two parts stores are correct and this is as built .
IGNITION CAP
IGNITION ROTOR
IGNITION CAP HOSE CLAMP
GROUNDS*/WIRING/CONNECTIONS THAT EFFECT SENSORS ECM(s)? and IGNITION ,FUEL ,EMISSIONS SYSTEMS
EMISSION CONTROL SYSTEM/COMPONENTS
THROTTLE BODY -mechanical condition as well as "maintenance" issues
VACUUM CIRCUITS/OTHER VACUUM LEAKS
EXHAUST SYSTEM -including possibly O2 SENSOR(S) wiring esp . AND EXHAUST MANIFOLD .
CHARGING SYSTEM/BATTERY(SOME ASPECTS OF STARTING SYSTEM )
SENSORS
HEADGASKET/OTHER COMPRESSION RELATED ISSUE .
The point here is to keep an open mind whatever you end up doing .So far we have eliminated the fuel filter and made less likely some other things .
Unfortunately we also have not so far , eliminated a single system .
( yes , I remember you have a functioning OBD2 system .)
Also this is not a judgement call or anything negative about what you have done so far - its just reality .
Now there are many ways to do this but since you now have the vacuum gauge we can talk about that .
The really cool thing here is in 20-30 min . of gauge work you are going to know A BUNCH that will help you neck down and hopefully eliminate the scarier PIA stuff .You will also be able to confirm/disprove much of your earlier work .