welcome to the board.
Tough decision to make, i have owned a year 2000 SPS (with Ohlins front forks) same as the 99 SPS otherwise, and curently have a 996R which has essentially the same engine and running gear as the 998FE.
Its a very close call, the SPS is a bit more brutal, bit more character! the testastretta engine in the 998 is more powerful, smoother and refined, but certainly not bland. On balance i would go with the 996R (but only just, the difference isn't as big as you may expect in my honest opinion). Lot depends on your budget, the new bike will depreciate more, and how much you value 2 years warranty.
For a more detailed comparison do a search here on the board on a story i wrote recently comparing the 2 bikes
"996SPS vs 996R Performance Touring Test" complete with dyno graphs of both bikes.
By the way the 996R does have the 998 testasretta engine, just in case you don't know.