Q: Removing the transmission by myself, I had a problem with removing the bolts from the flex plate.

Flex plates cannot be straightened or repaired in the field save for the possibility in some applications of replacing the starter ring gear if the teeth on the gear are damaged. If the flex plate is bent, a new one must be installed; do not use a junkyard flex plate. Flex plates are not expensive and they are easy to remove and replace. If a damaged flex plate is re-used the torque converter will not spin straight and that will destroy just about everything connected to the torque converter. The answer to your question regarding which components should be serviced now that the transmission has been removed from the vehicle frankly does not even depend on why it was removed given the mileage that you are reporting. If the transmission has 208,000 original miles on it and it is already out of the car, not only should the transmission be thoroughly disassembled, cleaned and refurbished (new clutch friction material, all new seals, new solenoids, etc.) but you should check the availability of various aftermarket upgrades (shift kits, valve body modifications, etc.) that are routinely available to re-builders once lots of field experience has accumulated with a transmission model. Using these upgrades often creates a phenomenal outcome but the success of a rebuild depends on following every single line of instruction in what is often a 100 to 200 page re-build manual. You cannot rebuild the transmission without the manual and every single instruction must be followed. The consequences of omitting even one step are simple: the transmission will not work. In practice, transmissions are easier to re-build than engines though because you do not need a machine shop and you are not measuring, and fitting, tolerances to within the nearest ten thousandth of an inch, however there are other caveats like you can’t get any lint or dust in the unit and thus the rebuild has to be performed in near clean room conditions; clearances in valves in the valve body are around .001 inches. If you are interested in a transmission replacement or rebuilding services, YourMechanic professionals in certain locales can assist with that. Please simply inquire based on your locale. If you have further questions or concerns, do not hesitate to re-contact YourMechanic.