Engine issue, when you come to a stop it idles down sometimes, other times it stalls out like it is flooded?

Hello, so it's mostly when you come to a stop the fault shows up, and the engine stalls. Since you have to push the clutch and brake pedal when coming to a stop, can you feather the gas pedal a little to keep the engine running? If so, then adding some air to the engine by opening the throttle plate might give some direction to diagnosing the issue. I know you replaced the Idle Air control valve, but the wiring diagrams show a Mass Air Flow sensor (MAF) on this engine, it will be on the air filter housing (air intake boot). Some MAF sensors can be unplugged, and the engine computer will run on a default strategy, that's something you can try. It would help to see some live scan tool data to see if any sensors are sending skewed data to the engine computer.
Did you clean out the ports before replacing the IAC as well? It sounds like the engine is lacking air when coming to a stop when the throttle plates are closed. So, if you can keep the engine running by giving it a little throttle when coming to a stop it will give an indication that there's a lack of air at idle.
Checking the spark plugs as well can tell you a lot about how the engine is running, if they have soot and carbon on them then you know it is running rich, if the plugs look normal, most likely it's not flooding out. Being able to restart it right away doesn't really sound like a lack of fuel, fuel volume and pressure would give you problems especially when the engine needs more fuel at higher rpm.

https://www.2carpros.com/articles/low-engine-idle

https://www.2carpros.com/articles/mass-air-flow-service

I would see what the spark plugs look like before replacing anything, just to get an idea of the running condition, if its a lean or rich issue. And you mentioned longer trips, does the issue go away completely when the engine gets warmer on longer rides? And the check engine light (or service engine soon light) is not on?
When shifting gears, you're doing it pretty fast, so if the engine RPM isn't dropping much during the shift, then it may not stumble.

Do you get any smoke from the tail pipe when attempting to prevent it from stalling out? When revving it up from the point of stall.

And you're not seeing any fuel leaking anywhere? Not around the base of the fuel injectors, to smell raw fuel like that sounds more like an exterior leak, a really rich running engine will cause smoke out of the exhaust pipe, and the spark plugs will have excessive carbon build up on them, and the idle starting to hunt if that's what you mean by loop, is something that happens when the ECM has trouble maintaining the desired rpm, a vacuum leak can cause that,
If you think it's a fuel delivery issue, checking the fuel pressure while running and then when the key is turned off for possible pressure leaking down fast would be one of the first tests I would do. If the pressure leaks down fast after the key is off, it can be the injectors leaking down, or the check valve in the fuel pump leaking down,

I just had a vehicle this week with a fuel pump leaking down after the key was off, and it turned out to be the pump assembly leaking down, and after a while of driving the fuel pump would only reach half the pressure spec it should have causing a no start condition.

On other thing you can check is the Canister Purge valve, if its stuck open due to a charcoal canister failure, the purge valve can actually draw fuel threw the Evap vapor system into the intake manifold, Ill try to find a picture of the purge valve for you. It should be on the driver side of the engine compartment, a 2-wire purge solenoid. With a red wire and a grey with yellow stripe wire.

Service info for the location of the purge valve solenoid is terrible, to find it you'll have to go by wire colors, but it should be closed when its unplugged and you shouldn't be able to blow any air through it. If you find that it's stuck open, and you might even find gas in the vapor line/hose coming to the purge valve, that might be the issue. But with a hunting idle, it means the ECM is able to control the idle with the IAC valve, if there is a vacuum leak large enough to where the ECM is closing the IAC fully due to excessive air coming into the engine you can end up with the idle up and down like that.

Here is a guide for surging type conditions:
https://www.2carpros.com/articles/engine-surges