Once warmed up, ours sits a tick below half way point on the temp gauge. Gets there within 5min (read it's hot as hell in California). I'm betting on a thermostat that's stuck open in your car.
As for less than smooth shifting on a cold transmission; sound about right. Plenty of threads on here about people flushing transmission/ diffs and it sounds like it makes the whole operation smoother, however it's 70-80k maintenance item. So at 45k it might be a bit too soon for it.
I'd look into the engine temp issue first and see if that also solves the transmission. Good luck!
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