It's a good idea to get a second installation of Xcode for this situation, in this case you need 3.2.1 with SDK 3.1.3 - I wish I could help you with a download link since it is no longer shown on Apple's page, but I have googled in the past and found direct, official download links which will work as long as you are signed in with your developer account, so good luck.
The annoying bit is that you need to go through your project files and set "Base SDK" to 3.1.3 and then back once you have completed the exercise. But it is the easiest way to flag what you can't do in 3.1.3. "sudo rm -rf" (I feel nervous even typing that) has an excellent method there but you need to have an inkling of what might be safe and what might not before you implement it or else you end up with code 10x the size it needs to be.
Apple really needs to sort out this issue - hopefully by flagging methods that are prior to your specified "Deployment Target", in the same way that deprecated methods are flagged.