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Ah, we have a terminology/interpretation difference going on here.
Most people think of an engine that hesitates as one that is running, but when the accelerator pedal is pressed a little, the engine fails to increase speed immediately, may even slow down a bit until it finally responds to the change and increases speed.
Ignition time is any time the key is in the run or start position, regardless if the engine is running or not, or if the engine is hot or cold. When the key is in the run position, the ignition system is enabled.
I don't think the problem is the ECT sensor anymore. If it was, it would lend to having a rough running engine when cold in addition to difficult starting (rough running due to too lean of Air/fuel mixture). You don't have the rough running engine once it starts, so I think that rules out the ECT sensor.
At this point, I would step back a bit and think about mechanical timing and cylinder compression pressures. Your cylinder compression pressures may be too low, and that could cause the difficult cold start issue, but allow the engine to run smoothly once it is running. Do you have an ability to check cylinder compression pressures?
Mechanical timing between the crankshaft and camshaft is also a possibility, but I would think it might also cause a noticeable change in how smooth the engine runs or how much power it has. Checking mechanical timing on a 5S-FE is a bit of a challenge, by how the engine sits in the engine compartment (no clear view through the camshaft sprocket to see the timing mark, unless a mirror is used). So this wouldn't be the first thing I would check.
How did your symptoms develop? Slowly over a long period of time? Or suddenly - worked fine up to one day, but the next, these symptoms were present and haven't changed much since?