I'd forget the cracking heads thing. I had a 2.5 Boxster previously and despite have some faults ('99 car) it was very good to drive, fantastic handling and robust build quality and thrilling engine notes throughout the rev range.
You should get what you pay for if you shop carefully, I bought a mid priced boxster so had to correct a few things. They are reliable but have certain charactertristic faults, RMS (£580 to replace at an indie) and cracking header bottles, same sort of price.
On the front of cracking heads its not something I've heard of and likewise what I have heard abot the S2000 is they are bullet proof and very reliable. Yours may have been a bit of a lemon, its certainly not a typical story. I test drove a new S2000 prior to buying my 911 (it was a good excuse to test drive lots of sports cars!) and I really really liked it. So much so that I believe pound for pound the S2000 was the better car........but that was in comparison to a '99 72k 2.5cc car. The 3.2 is a whole different ball game. My Boxster followed a MR2 turbo. I don't think it was any quicker but the difference in handling set the two apart. Don't let the head thing put you off. I suggest you go to a OPC or indie and get some warranty with it to negate any concerns, the Boxsters are great cars but I do have a soft spot for the S2000!