You wont' do any damage by polishing with a UDM/PC/Flex/Cyclo. If you can clean up your paint and correct all the imperfections you should. then just make sure you maintain the car properly, wash it bi weekly/monthly ...if you washing technique is good (clean mitts/drying towels etc) then your paint should hold up quite well.
Waxing monthly maybe a good idea as well. GL with your S2000!