Dave,
I love Boxsters. We have two of them. They are a lot of fun to AX, they handle really well and my 2006 S has lots of HP and torque. The downside is that they can be very expensive to repair. Older Boxsters are being driven more and more on tracks and a lot of suppliers are coming out with more track specific parts and improvements for them. You still need to spend about $25 - 35K to prepare a spec Boxster.
I love 911's. I've owned a couple of them. They are the most fun and challenging to drive. They can be very expensive to set up and repair. I chose to run 944's because I could get more bang for the bucks. I'll probably get another 911 in the future because I just love driving them.
I love 944's (Do you see a trend here?). They are inexpensive to buy and relatively inexpensive to set up for track racing. You can spend $2500 (half the cost of your rebuilt motor) for a 944 in good running condition and drive it in GSS as you learn the car and slowly modify it to suit your needs, budget and goals. A fully prepared Spec 944 can be had for $10 - 15K depending on what you want to do. I was able to buy a motor, have it gone through, with new rod and main bearings, a used crank, misc. other parts, and all new seals and have it installed in less than two weeks for less than $4k. Keep in mind that mine is a much rarer 944S. 8 valve motors are much easier to find and less expensive.
We had 19 944 drivers at the last AX. A well driven 944 Spec or GP class car can compete with almost all of the cars at an average AX and can get into the top ten or even win BRI.
On the big tracks, they're as much fun as your Boxster and will run similar or better times. If you've ever wanted to know what one feels like, I'll be happy to take you around at an AX or one of the tracks. Ask Jackie Corwin, John Kincaid, Sean Steele, Morgan & Ron Trotter, Tim & Tony Comeau or any of the other 944 drivers how much fun these cars can be. You'll learn more about driving and car setup than you ever imagined.
Just my .02. Good luck with whatever you decide.