Greetings all, first time poster, lifetime reader.
The back story.
This vehicle was given to me by my brother as a spare or backup with 220xxx miles on it, 202656 on the odo.
He purchased Merlin in Illinois in 2006 I believe with 180k on it, give or take. He told me it was a runner, for all intents and purposes. It sat on my farm for one season(Michigan) until its calling came when my 96 Bonneville went down.
Took it for a test drive after putting black Bonnie's battery in, only to find a wicked gas leak.
Replaced gas tank and sending unit, transfer pump with rockauto/ac deco equipment. Gas gauge hasn't worked since. It's the least of my worries.
Due to lack of specialty tools and funds, I have been unable to determine fuel pressure.
I just replaced the cat, old one was swiss cheese, but I can still hear the slightest pinhole leak from what I think is the exhaustanifold downpipe. The o2 sensor wiring is cobbled, I haven't had time to rewire and heatshrink. The connections are sound, but exposed to contamination.
Diagnostic codes thrown previously was 1-1-3 , one if the most vauge from what I researched. After replacing the cat, the only code registering is 2-3-1.

What I am experiencing with engine @ temperature on a 70degree day in the afternoon:
Rough idle between 700/900rpm (inconsistent, not just surging)
On acceleration from stop there is hesitation that feels like it might stall if not expertly footed (and has)
When entering highway speeds WOT feels like it's being choked, not enough fuel or too much air( bogs down until less pedal applied) .
Shift timing gets a little funny, stick around 2500-3k for a second before shifting( vacuum leak?)

American muscle gas mileage without the performance.
What I experience on a brisk 50degree morning with a freshly reset ecu:
A brand new vehicle.
Save for the slightest if any hesitation off the start line, I can WOT and it feels like I'm in my Integra.
Also replaced ECT sensor on a whim. Side note really.

My suspicions are down to a few items:
Mechanically; main fuel pump, FPR ( no gas smell present, need to vacuum test), fuel injector leak, cold start injection leak, fuel check valve.
Electronics; TPS, IGN coil, ICU,Luck
I have tried two separate good AMM, same result as well as another ECU with same results.
It runs well until the CEL comes on. This has been the issue since my brother went on a 3k mile rumspringa across the US, he should have rebuilt the whole thing when he stopped at IPD!
I'm sure I left plenty out. My ultimate fail, I'm a licensed 12v tech, and I haven't performed the checks to make sure everything is communicating properly. I have a 8month old, and 3.7 year old, my wife and I work opposing 40 hr weeks, I'm not lazy, I'm well motivated, just tired. This was a project car turned DD since early winter 2014.
If you've read this far, thank you. I will be updating as I propser with pictures and possibly answers. I'm not here for answers, just understanding and brainstorming. My theory is, if you can't fix it yourself, you shouldn't be driving it.