I\'ve downloaded the final version (and never installed any beta versions before) of xcode 3.2.3 with sdk 4, and now I can\'t seem to find a way to compile my app for a 3.1.3 iO
As it is, you can't. They probably did this on purpose to discourage new apps compiled for 3.1.3 which foils multitasking.
Instead you can compile for iOS 4 but make your deployment target 3.1.3. This doesn't really require any more real work, as long as you don't use any non-3.1.3 methods/classes etc. and the application can install and run on a 3.1.3 device. You can also then make your application multitasking aware so that it works nicely on a device that does run iOS 4 and is capable of multitasking.
Just a note: the Base SDK may be set at the project level, but you will need to go to the build settings for the target itself to set the deployment target (that setting is not available at the project level).