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The thermal timer has nothing to do with the pump... it simply supplies ground to complete the cold start injector circuit if 1) the engine is cold enough, and 2) the ignition hasn't been on for more than 8-10 seconds. The pump relay is controlled by the ECU without input from the thermal timer.
I can't see not pre-running the pump as causing any real problems, but according to Ben Watson's How to Tune and Modify Bosch Fuel Injection, it is supposed to run 1-2 seconds whenever the ignition is switched on.
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