I have a 3G with 3.0. I've created a jailbroken IPSW for 3.1 with pwnagetool. Is it okay to install the IPSW using Upgrade, instead of restoring, so that my data is preserved without having to restore from backup? Or will this fuck something up?

Make a backup and try it. If upgrading fails you can enter DFU mode anyway and restore to 3.1 and after that restore all your data and setting.

Upgrading didn't work for me. iTunes 9 gave me error 14 and error 9 I think. But iTunes 9 is a bitch anyway. As a sidenote: 3.1 kinda messed up my CarrierBundles. I'm on the official carrier for Germany and it wont show me any carrierlogo nor that it is connected to the cellular network. Signalbars are up anyway and 3G works.