There are two different issues in your post that I'd like to address;
1. Lots of unplanned maintanence
2. Desire for a manual S model
#1 is going to be roughly the same for both a base or an S model (given the same year and mileage). More important is getting a PPI so you know what to expect. A well maintained car will sell for more money than one that will need a lot of work - at the end of the day its hard to say which car will be cheaper overall. Some folks are willing to pay more up front to avoid repair bills and some (like me) are happy with a car that needs some work because I do most of the repairs myself or can get them done somewhat cheaply. The key point here is that the PPI will help you to set your expectations so you don't have any surprises (surprises are what seems to irritate owners the most).
#2 is really a personal decision - although almost everyone on this forum will agree that more power and a manual transmission is a good thing!
Best of luck and let us know what you decide to do...