The problem with your engine temps not staying high enough can be credited to the thermostat. Modern thermostats are designed to stick open when they fail, and yours has failed and is stuck open

The thermostat never closes, so cool coolant is always flowing through the engine. This is especially relevant on the interstate because the radiator cools the coolant much more effectively from the extra amount of cool air blowing in at higher speeds. Replace the thermostat to fix.
The specific problem with your transmission eludes me. I guess it's MAYBE possible (this is a big maybe) that the engine not getting up to full operating temp is affecting the temp of the transmission fluid and causing weird shifting. However, your transmission is electronically controlled and the engine temp technically shouldn't have any effect on it. If it was one of the older style centrifugal-force automatics, the temp might have some effect. In this case, if swapping out your thermostat doesn't magically fix it, ask someone qualified to give you a proper answer. I'd call a Toyota dealership service department and ask them. They might want you to bring it in, but on the other hand they might tell you what's causing the problem. You might try consulting a Hayne's or Chilton's manual for your car, too. If all else fails and no external reason can be found... it's time for a transmission rebuild.
Did the A/C blow cold last year? If so, the problem with your A/C can be attributed to two possibilities:
1. Low refrigerant due to a leak. Replace seals or leaking lines and recharge the system to fix. This is the cheapest possibility and should be tried first.
2. Dying A/C compressor. Replace A/C compressor to fix. If you recharge the system and there are no leaks it's definitely the compressor.
Good luck