Richen the low speed needle 1/4 turn and retest to see if the hesitation goes away. If you still have it, richen another 1/4 turn and retest. You will probably need to adjust the idle to keep the engine running after richening the low speed so much. It sounds like you have the low speed too lean and it's lean bogging under acceleration. Just keep richening the low speed needle until the hesitation goes away. Once it's set you can then adjust the high speed needle setting if it needs it for top speed.
DO NOT adjust the "3rd needle", that's the spray bar and affects the entire throttle range. You need to adjust both the spray bar and low speed needle at the same time when moving it and it only makes very fine adjustments to the engine's performance. It's set at the factory and almost never needs to be moved. Resetting it if it's been adjusted can be a pain if you don't have a great deal of experience tuning engines.
As for the temperature, tune the engine for best performance and then temp it for a reference number. I usually don't temp my engines and just tune for performance. So many factors can affect the temp of an engine while running. A well tuned engine will run at one temp in one set of weather conditions and another temp in different weather conditions.
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