Engine surge, sputter and misfire.

The car had sat for a number of years before I bought it. It had some severe running problems, but I felt confident I could figure it out. I am stuck.

The car had a severe miss and would surge and sputter. Getting it up to 30 mph was a problem. I replaced plugs, wires, cap, rotor and coil which helped a little. I checked the idle air control valve and it does work. I replaced the EGR valve, fuel filter and air filter.
Because the car sat for several years, I thought perhaps the tank at some point was very low on fuel and maybe the fuel pump o-rings had dried out, so I replaced the fuel pump.

That was a huge improvement. At highway speeds the car runs fine. No misfires and only the occasional sputtering. The problems that remain are as follows:

Hard starting. Seems to be flooding now. Have to step it to the floor to get it to start. When cold it runs fairly smooth but as it warms up it has a slight misfire and surges a bit.

At lower speeds with slight acceleration it sputters and misses just a bit and when coming to a stop it will stall. Again, I have to hold the accelerator to the floor to get it to start back up. If I keep one foot on the brakes and one on the gas it will keep it from stalling but it still misfires.

Last symptom is erratic shift patterns. It will shift fine when cold and most of the time when warm. However, at times it wont shift out of first until between 25-30 and when slowing down from highway speeds you hit about 40 and it will abruptly shift down, but not every time.

While trying to trace some vacuum lines, I removed the air filter assembly and found the new filter was stained and smells like gas. It is clearly flooding.

I pumped smoke into the intake and could not find any vacuum leaks, but I suspect that is what it is given how the transmission sometimes acts.

Any guidance would be appreciated.