Why does truck start great, run rough when warm, then great at normal temp?

It could be many things, unfortunately and without experiencing the problem first hand or being able to do some basic diagnostic tests its hard to say. Start with the basics, have the spark plugs been changed recently, (if changing them check that compression is even and the plugs coming out are even in color none fouled or damaged) check the valve clearances (often over looked) make sure there are no vacuum leaks. Then check spark plug wires, distributor cap and rotor to see ignition system is in tact. It's hard to check the injector (or ignition) without a scope, or to see if there is carbon on the back of the valves. If the check engine light comes on you need to retrieve codes, its easy on OBD1 Toyotas. Check this link http://www.troublecodes.net/Toyota/

I can think of the water temperature sensor turnes the choke off too late or too early or does not working at all.

it cold be a sensor problem but i would look at the stored codes first that would give you idea where to start most shops will do that free or at a low price.