It's a 12-year-old car, so all bets are off. All the things you mention are easily fixable.
Hard shifting: change transmission fluid and filter. It's supposed to be changed every 60,000 miles, and Haynes says 30,000 miles.
Temperature: you're on the right track by flushing the system, changing the thermostat, and checking the sensor. Replace the sensor, and also check to see that the fan motor isn't corroded, or doesn't have some blockage. It's just something you haven't thought of yet.
The blower fan is either a fuse or a rheostat switch. Use a voltage tester.
Dull headlight lenses: use rubbing compound on the plastic lenses to polish out yellowing discoloration.
Broken cup holders and air vents: get real.
These are all common issues to be expected on a 12-year-old, high mile, used car. If you're not up to it, it might just be better to buy a new (er) car and make the payment.
Actually Ford made a total piece of junk. The car has a BIO-DEGRADABLE Wiring Harness! Fact of life, the wiring harness's disintegrate after a few years. Ford recalled to the original owner only, 100k miles or 10 years. The cars have shorted wire everywhere under the hood. Replacement harness is the same crap and is $2,000 to install.
I have absolutely every single problem with our 96 Mystique, except that my transmission problems haven't gone away with a trans service done at the dealership.
As for the blower only blowing on high, you need to check the blower motor resistor as this controls fan speed and eventually WILL burn up your fuse block. Trust me on this one!!! I had this replaced under recall and it did it again 2 yrs later. I guess they just replaced it with the same POS.
I really shouldn't complain too much; the car does have 167,000 miles on it. Good Luck.