Greetings fellow new Boxster owner. Being a new owner, I'm probably still seeing ownership through rose colored glasses however, allow me to share with you some of my thoughts, and research. When the later 98-99's came out they suffered from the 'slipped sleeve' issue, from what I've been able to gather, Porsche did a silent recall in that they replaced the engines while trying not to make any noise. Regardless, not getting off on the right foot with customers. The other issue, IMS failures, seam to occur on a percentage of horizontality opposed Porsche engines, we'll have to deal with them but there seam to be a few things as owners we can do.
When my wife and I researched our purchase, we "sampled" the market on E-bay. What we would do is search Porsche>Boxster>1997-2004>sort from lowest price. I no longer have the papers I jotted down the info on so I don't have hard numbers but basically we were looking for 'rollers' and found very few. Most of the rollers were unfortunately due to vandalism
One was due to flooding. Plenty of wrecks, and lots over 100k on the odometer. In short, while there is a risk, the cars are great drivers, the prices have dropped dramatically, making now an attractive entry point!