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I said the EGR doesn't appear to be the root cause of your issue. The EGR appears to be active at a state where it should not be, so the EGR is causing (in my opinion) the idle problem. But from what I can deduce without actually personally diagnosing your car is that the throttle position sensor maybe the cause of why your EGR is active when it should not be.As you say, EGR is likely not the source of the problem. I still plan to remove and clean it so that I can rule it out as a possible issue.
I’ll look into the throttle position sensor (calibration as well) and the coolant temperature sensor. Is there any simple way to diagnose an ECU as being potentially faulty? My imagination would be that these are expensive and difficult to change; I’ll do some research.
Aside from not being able to pass emissions, is there any negative effect to continuing to drive with the deactivated EGR? Am I going to ruin my Catalytic converter by sending unburnt fuel into it?
Your fuel tank should be under some pressure - the vapor pressure of the fuel. In winter, your gasoline will have a higher vapor pressure than in summer, as winter gasoline needs to additional volatility to ignite in cold winter temperatures. But temperature plans a major role in gasoline vapor pressure. The vapor pressure of gasoline drops as the temperature drops. I don't know where you are located, so unless you live in a relatively warm winter area, you really shouldn't be noticing significant fuel tank vapor pressure. Your EVAP shouldn't be considered faulty if your fuel tank has a high pressure - EVAP is not meant to control fuel tank pressure.
If your coolant temperature sensor is faulty, your car should remain at cold idle speeds well after the engine has warmed up. Does it? Is your coolant temperature gauge in the normal location after the engine has fully warmed up? Also, if the coolant temperature sensor is faulty and reading too cold (keeping you engine idle speed higher - but still steady), your EGR should not be active as the engine doesn't think the coolant temperature is above 140 deg F. By how you previously described your engine's operation, there wasn't anything there indicating a coolant temperature problem.
Unfortuantely, an ECU doesn't know when it has a faulty capacitor. Toyota's built in the era of yours are notorious for having ECU capacitor failures. Sometimes when taking an ECU apart, a faulty capacitor can be identified (it has leaked and also the corrosive leak may have permanently damaged your circuit board too) or the capacity may have swelled a little. Often though, a capacitor has no visual signs of failure. It is difficult to test capacitors for failure when they are installed on a circuit board. They are easy to diagnose if removed from a circuit board. But most folks are not up to going that deep into an ECU.