Rough idle, bogs down sometimes at stops?

Car has been acting very randomly with the same problem going in and out with increased frequencies.

Noticed first that I would be driving around and suddenly the car would bog down. Sometimes at stops, sometimes while driving, then would kick in all the sudden and be fine.

My first thought was:
1. Spark 2. Fuel 3. Air

I first went the cheap root and replaced the spark plugs and air filter, they needed to be changed and new it should be done anyway. Ran better for about three days then back to the same issue.

I next thought fuel since it was stuttering in and out and very apparent under acceleration. Since this car did not have a fuel pressure fitting on the rail (blarg), and I had spent many days trying to find a fitting, I gave up and replaced the fuel filter first, not better. Got mad, replaced the fuel pump. It ran better, but did not solve the problem.

I rechecked the spark on the car and it was okay, went ahead and re-gaped the spark plugs, replaced the distributor cap and rotor and it seemed to idle better, especially after adjusting the throttle cables, but still was bad under acceleration and bumpy idle.

I was then thinking catalytic converter. I drilled four holes in the converter to see if that would help but it really did not. Plugged the holes with some liquid steel and back to the drawing board, yes I plan on replacing it soon, granted I can get it running right.

I was fed up. Went to the junk yard and found a fuel pressure relay and tried switching it out, no better.

Fed up more, I took it into the dealership to have diagnostics ran on it. They told me it was fuel injector #2 and wanted $350.00 to replace it.

I got online, ordered genuine fuel injectors and went ahead and replaced all four of them this weekend. After adjusting the throttle cable back down to normal, the car was running great like it was before.

I drove the car somewhat aggressively to a friends house, stopped the car once after driving twenty miles, drove another ten miles after that and all was good. After the car sat for about two hours, came out, started the car, and it was idling rough again and doing some weird stuff again. Only this time it would actually accelerate fine when pedal depressed pretty far down but still not running right.

I am not sure what to do now, the only thing left on the fuel side is the fuel pressure regulator, which is like $140.00 from the dealer, and like $95.00 online. I am not sure what to do next. It almost makes me feel like the actual ECU is bad or something. If it was anything else major, I would imagine that the codes ran at the factory would have told them something else they would have mentioned to me, like O2 sensor, etc, etc.

I imagine after it setting two hours in cold rainy weather it had plenty of time to cool down if it was heat problem, and if was just cold, that it would have gone away the thirty miles I had to drive home. Help!