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.

There is a quick and dirty way of doing thing and oddly enough it will be the cleanest.

I recommend cp'ing everything onto your external volume. Just get everything over there and make sure the sizes of the folders match.

I also recommend then to chmod -R 7777 on that volume so that you can carry, copy, and do whatever you need to when the time comes later.

Once your file are transferred and chmod'd, erase the drive you want to be used for the OS and install a fresh OS. Set up the new user account and drag over the items you need where you need them.

Once all that is said and down, reboot to the installer and reset permissions and ACLs for the main drive and that would reset things back to 700 for the ~ folder and fix any lingering things.

This is coming from YEARS of fixing this kind of a mess for people (strangers, friends, and family). You can take what you want but it is better to reduce the steps and keep things simple. Starting fresh will prevent issues down the line. Trust me!

All the best!