iOS firmware 4.1 breaks your jailbreak and should not be used yet. Please wait for the 4.1 jailbreak before updating. You will certainly lose move by updating than you have now.

iOS firmware update v4.0.2 or 3.2.2 for iPad breaks your jailbreak!

Absolutely do not update your firmware in iTunes! This update does nothing except break your jailbreak! If you have to restore, make sure you use Saurik's server with your stored SHSH so that you can restore 4.0.1 firmware.

For the safari pdf security patch offered in 4.0.2, you can install Saurik's patch for this by installing PDF Patch in cydia.