When you do Jailbreak, and install Cydia, the shsh is automatically backed up.
If you want to upgrade to iOS4.1 (never 4.2!), you can find from http://www.redmondpie.com/jailbreak-iphone-4-3gs-3g-on-ios-4-4.0.1-and-ipad-on-ios-3.2.1-with-jailbreakme/ alike to download the old iOS. But, you may need to find iTune 9.4 or 10.1, not the latest iTune for the same reason as iOS 4.2.
You MUST put your phone into DFU (direct firmware upgrade) mode in order to avoid iTune control! DFU can read any firmware, not the latest one Apple force on you.
http://limitededitioniphone.com/how-to-put-the-iphone-into-dfu-mode/