backups vs upgrades

[miamicanes]

I'm getting ready to do my first upgrade (from Sprint stock ROM to Helmi's AKU3.5). However, I'm concerned about the guide's instructions to "back up" my data. Specifically, what do I need to do BEYOND merely sync'ing to save things like old SMS messages, my call history, photos I've taken, etc? Is it enough to just sync, then navigate to the phone's folder in Windows Explorer and indiscriminately copy everything in it to a folder on the PC's hard drive (or zip/rar it)? Or are there things I'm guaranteed to lose regardless of what I do, and other things that I have to do something non-obvious to back up?

For example, I have a ton of old SMS messages. I'm a packrat, and hate to delete anything. If I can't preserve them across the upgrade, can I at least dump them to some kind of human-readable file that I can print out and keep around indefinitely? Also, I'm bad about abusing the phone's call log in lieu of creating proper phone book entries for people I call. Is there any easy way to dump that log to a text file before blowing it away? Ditto, for things like saved PIE usernames/passwords, cookies, etc.

Also, are there any things that will be backed up, but can't be used by AKU3.5 or WM6 because the data format itself changed somewhere along the line?

Basically, I want to burn as few bridges behind me as possible, and feel confident that I know which ones WILL be burned regardless before I actually do it