Yes, you can lower the rating. It is not officially supported, but I did it on two 3G with success for testing on 3.1.3.
First, find a tool called RecBoot called the0rkus that only works on Intel Macs. This will cause the phone to exit recovery mode after downloading software 3.1.3.
Find the .ipsw file for your device, as you know, this is another file for iPhone 3 / 3GS or iPod Touch. Download this software to your phone via iTunes in the usual way, holding the selection key while pressing "restore". Wait for it to load.
When it finishes and reboots, you will find that iTunes is complaining about the wrong version. The situation - this software is downloaded, ready to go, but it lacks Apple’s last blessing. RecBoot takes it out of this mode, “waking up” the phone to its normal state of activation readiness. After you connect to iTunes with a SIM card inserted, you have a phone just as if you hadn't gone to 4.0.
Too bad, we have to resort to hacking for testing with old devices, but I do not know another way. It would be nice if the simulator could still run 3.1.3, well, if setting the deployment target would point to functions up to 3.2.
You can also install the old Xcode 3.2.1 with the iPhone SDK 3.1.3, but the hardware is a true test of whether your software really works. Given this, you can probably skip searching and using it - although there is no faster way to find everything that you cannot use in 3.1.3. There are no problems with having multiple copies of Xcode of different versions, but it is recommended to remove them using the script provided in /Developer/Library/uninstall-devtools (read the readme included with each Xcode distribution)