How do I rebuild my HDD/SSD from scratch without Time Machine on MacBook Pro?
If the Users directory on the SSD is the same, ie., you haven't changed files, etc., then it is still the Users directory that the OS is using. However, if you did some terminal magic to make this transition I could see where things would get a bit hairy.

I'm not as familiar with the terminal, but I can tell you what I would do in this situation. I'd clone disk images of each drive to the TB using Carbon Copy Cloner or some similar piece of software. At least as a disk image you'll maintain the integrity of the files - I'm not sure how this is effected via encryption though. It may not even work.

Ideally, you'd reinstall OS X on the SSD and then use your Terminal magic to move the Users directory to the HD - if that is still your plan - mount the disk image files and move files accordingly, this should help with permissions. Again, I'm not sure how the encryption works into this either. And I've not seen many instances where moving the Users directory didn't result in some kind of mess. If you can keep it on the drive with the system, I think that would be best. 

BTW - Lion should've installed it's recovery partition locally when you did the original install. 

Perhaps not much help - but some things to think about.