Your best bet would be to invest in PKGBackup (Cydia, $7.99, USD). Yeah, it's expensive, but it sure helps in backing up all your Cydia apps, tweaks and settings. It's very handy to have when it comes to restoring.
It's not perfect, especially when making the jump from iOS 4.2.1 to 4.3.3. I had to fiddle a bit with the iPad to get it exactly as it was before I upgraded. However, it still downloaded all my tweaks and stuff - I just had to [mostly] rearrange the springboard.
It's also handy if (when?) the day comes you have to restore to the same firmware. Talk about a timesaver! Yeah, you can just manually reload everything, but as you said - painful!
Once you've got everything backed up (including your App Store stuff in iTunes), I'd suggest you just upgrade the iPad to stock iOS 4.3.3. Then, go to JailbreakMe 3.0 (via Safari on the iPad) and do the real easy two click jailbreak. Then, put everything back on from the backups.
Of course - I'm assuming you have SHSH blobs for iOS 4.3.3. Else, I'm afraid it's a tethered jail break on iOS 4.3.5 for you.... Oh, and no matter what you do, you will "wipe out" all your jail break stuff. Cause you have to go to the stock firmware before you can jailbreak, regardless whether it's 4.3.3 or 4.3.5 (stock = no jail break tweaks/fresh out of the box software...).
Hope this helps and good luck.
Marilyn