Also, the 998 motor won't exactly work in your bike without buying the proper wiring harness, ECU, throttle bodies, airbox and likewise many other parts. It will fit, no problem, it will eventually work with no problem, but you've gotta do a complete conversion.
If you're dead-set on keeping the bike, its a smart idea to do the conversion as well, the 996's and 748's were notorious for chewing up rockers, even after replacement. You might wanna look on ebay and see if you can score a used motor, wiring harness, ECU, throttle bodies and airbox. Usually people parting bikes/motors, have all the parts you need.
Then you can take the motor bare, already out of the bike and give it to the shop thats currently working on your bike. Have them re-build it and you should be good to go. YES it will be costly (few grand) but when you're done, the bike shouldn't ever fail again. Key word here... "shouldn't". On the other hand, for a grand, you could fix the 996 and be back on the road. Sell the bike, get your money out of it and buy a nice used 998S or 998FE (later model years are better) and be done with it. The choice is up to you!