[The Radium King]

go 's'. if nothing else, I would expect it to be more reliable (more brakes, more water cooling, more oil cooling, stronger internals).

maintenance budget depends on how much you can do yourself - off to the mechanic for every sneeze, or search out the issue on forums like these, source good used parts online, and put them in yourself.

mileage isn't an issue so much as year of purchase. some might actually say higher mileage is better, as the car will have been run past the standard ims failure point with no ill affects or failure addressed. do some research on this forum to find the 'good' years for this car with respect to dual vs single row ims (2001 to 2005 have the highest failure rates; 2000 and earlier and the 987 series have stronger bearings).

can't speak to auto trannys but the 6-speed (which comes in the 's' model) is a strong unit. the 5-speed is weaker, but is paired to the weaker engines so should be ok.

can't say about glass windows - i'm a 'get the car as light as possible guy' and live with the plastic.

me, i say get an early 2000 S; first year of the S, they made lots of them, there are lots for sale around your price point, and the early ones have the good ims.