Ahhh, it feels so damn good to be on 4.1.
It's also running quite a bit smoother than 4.0.1 did. I think I just had it too bogged down.
So here's basically what I did, in case others want to follow suit.
1) Make sure that all App Store and Cydia apps are up to date.
2) Purchase PkgBackup from Cydia (you can try the free AppBackup + AptBackup, but those totally failed for me. They'd both crash back to SB right after launching.)
3) Run PkgBackup to take a total inventory and backup of aaaaaall Cydia apps and settings. As a bonus, if you also have SBOrganizer and CategoriesSB purchased, PkgBackup, which is made by the same dude apparently, will backup your SB layout and custom folders, respectively. I don't use CategoriesSB, but I do use SBOrganizer, so that was an awesome bonus.
4) Perform a final iTunes backup+sync. This not only backups up your official apps, contacts, and settings, but also backups PkgBackup's backup, since it sneaks itself into "official iPhone data" somehow. :lol
5) Use TinyUmbrella to perform a managed restore (not upgrade) to 4.1 via iTunes, which 5installs iOS4.1 but blocks the baseband update, retaining my phone's unlock-able quality.
6) JB using limera1n. Easy-peasy. Install Cydia. Download PkgBackup from Cydia.
7) Perform a full restore-from-backup via iTunes to restore legit apps, contacts, settings, etc... and the PkgBackup data.
8) Run PkgBackup and select to restore from the backup you made in step 3. It connects directly to the relevant repo servers and downloads all of your Cydia apps for you. It'll elegantly skip apps that are blocked due to firmware conflicts, or downed/hammered repos, and move on down the list. It essentially keeps a checklist, letting you know how many apps were successfully restore. For me it was 110/120. Later attempts to re-restore from that backup eventually got the number up to 117/120. 3 remain incompatible with 4.1, so PkgBackup can't do anything about those.
Now I'm good to go. I didn't have to manually redownload any apps save for PkgBackup and the 5.0 beta of BiteSMS. I didn't have to reconfigure any of my Cydia or App Store apps. I didn't have to reorganize any of my folders or layouts, except for Game Center, which didn't exist on my iPhone before so wasn't part of the saved layout stored in PkgBackup. Now I think I'll perform that SSH surgery and swap out my BiteSMS icons.
Woooooo!
Edit - Uhh, should I "update" my JB to the newest beta and/or release candidate? I used beta 4 last night.
Edit 2 - And for those of you that noted my horror story a few pages ago, all of that was, amusingly, related to the official 4.1 update segment. But learn from me. Uninstall the Windows/Mac/Linux/Whatever WiFi Sync component before attempting the update. Something about it breaks Apple's/Cydia's/TinyUmbrella's/whatever's ability to authenticate the restore.