32 GTR's are getting old, so it's normal for things to break and wear out.
Bushes are a common item that will be worn, the gearbox, if it's had a hard life, will begin to show signs of worn synchro's, suspension is usually replaced with coilovers but they can begin to leak if they're old, window seals will start to deteriorate...
Great cars, though. Once you get the RB26 rebuilt and tuned with the new turbo's, you'll fall in love all over again.
Any car will cost you money in the long run, anyway. Even buying a R34 GTR, things will break... maybe just not as quickly.
Edit: $9k for a rebuild? That's pretty expensive... you must be using big-brand name everything and need a new crank, etc?