Ok, this tutorial is exclusively for iPhone 3GS owners with old bootrom who want to switch to jailbroken iOS 4.0.2. To do this tutorial you need a Mac and an iPhone 3GS jailbroken on iOS 3.1.2, otherwise you won't be able to restore. You cannot restore from a jailbroken iPhone 3GS with Spirit/jailbreakme.com because those jailbreak solutions are userland and not made through bootrom. However, if you have an iPhone 3GS with an old bootrom, iOS 3.1.3 and jb with Spirit, then you can install Spirit2pwn from Cydia, then load the custom firmware made with this version of pwnagetool.
I haven't managed to make the tutorial yet, so for now I can't confirm if it's good or not, if you have SHSH saved you can test it without worry.
Step 1
Download this modified version of PwnageTool from here.
Step 2
Download iOS 4.0.2 for iPhone 3GS by here. If it is saved with the extension .zip then change it to .ipsw.
Step 3
Open PwngeTool and make a custom ipsw, you can find a tutorial for this here. Select iOS 4.0.2 and not iOS 4.0.
Step 4
Change the custom ipsw extension to din .ipsw in .zip and replace the file kernelcache. release. n88 with the one from the PwnageTool archive downloaded in step 1. After that, rename the custom ipsw to .ipsw and use it for restore.
Step 5
If after restarting Cydia it doesn't show any source, then go to sources, add the source: http://apt.saurik.com/cydia-3.7. After adding it, all sources should appear and everything should return to normal.
