My '98 Saturn (114K) overheats when in bumper to bumper, engine light goes on, then I can't seem to shift into fourth gear. When it cools down it's okay. Coolant was just flushed & levels look okay. Transmission fluid was replaced @ 65K. Is it my thermostat?
No. A stuck thermostat would either cause overheating all the time or would run too cool.
First make sure the serpentine belt is in good condition and properly tensioned in order for it to drive the waterpump properly.
More than likely it is something to do with the cooling fan. Coolant temp sensor, relay, wiring, connections, fuses, and the fan motor it self are all possible culprits.
Turn the AC on (it must be fully charged and operational) and see if the cooling fan comes on.
If not start by checking the fuses in both fuse boxes. Use a test light or ohm meter if there is any doubt.
Next check the relay by substituting a known good one (from the AC for instance).
Next is the coolant temp sensor (ECTS). If it is original replace it. Check it's connector also. They can corrode and prevent proper operation. See http://www.2carpros.com/forum/saturn-sc-1-1995-vt4925.html?highlight=ects for more info.
Lastly put 12 volts directly to the fan motor to see if it runs.
Get this first issue resolved and see if it solves the shifting problem. If not you will need to have the codes pulled and post back.