On a earlier version of Mac OS X, I tried doing a similar thing with my Applications folder to put it on a different drive to conserve space. After copying the original /Applications to the new drive, I replaced the original with a UNIX soft link to the new location. This worked fairly well for the most part, but future updates of some Applications, and installers, did not play nice with my soft link. So, I abandoned that approach and ended up just getting a larger hard drive that could fit every thing.
I really like your idea of putting large data files/libraries in your User home folder to a bigger, slower HD, and keeping the main operating system and applications on the smaller faster SSD, that is a very good idea, and an obvious way to maximize the performance of your system that, without question, anyone knowledgeable about computers could clearly recognize.
Because the operating system may have certain required folders for /Users and their ~/ home directories, even using the underpinnings of UNIX to trick it might not work, though it should. Some UNIX things may be overridden by the Mac OS, I am not really sure what is going on there.
Maybe you can consider a hybrid approach to this...inside the normal OS created /User/home folder, create one UNIX soft link, or Mac alias on the SSD to point to a folder on the other HD, then just organize that folder as you want. I think as long as you have the /Users/home folder unchanged, and that is a regular folder instead of an alias itself, then whatever you put in the aliases folder within that ~/ folder, should be fine. Maybe not the ideal approach, since you have one additional layer to go through, but /Users/home/a/Documents, is not too bad, where your ~/a is an alias that points to /HD/a or whatever. (Don't move your ~/Library)
Not really a solution to your original approach, but a work-around. Sounds like some of the problems you are having are due to the file access permissions, and not sure that I can give advice on how to fix that, since I don't totally understand what you did.
