There are error codes stored, you need to get a code reader and find out what they are. The cruise control will not work with errors present. I suggest reading the codes, deleting them and then see which ones come back.

The early 5 speed trannies were/are problematic. The software used to run them was not paired well with the car, which is why there are so many updates.

You also need to take a look at the electronic throttle box and see if the lable is white(bad) or yellow(replacement, better).

By all means, flush the old ATF. Toyota dealers sell it at a reasonable rate. You will need at least 10 quarts to do it right. The dipstick for the tranny is under the air intake and hard to see, but it does have a yellow handle. A home flush take around 30-45 minutes. I would do the modified flush: Drain the sump with the tranny cold. It uses an aluminum crush washer, the same as the oil pan. Then refill through the dipstick hole to get to the same level as before. Then perform the 2 quart at a time flush using up the rest of the 3309 fluid.
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