Problems with SSD boot install

Despite extensive reading on how to create an SSD as a boot drive, my confirguration is buggy. Intially boot up was lightning fast and everything seemed to be running well between my OS-based SSD and my User Directory-based HDD. But at some point something when wrong and now I get impossibly slow start-ups and hang-ups during use. Maybe someone here can help me troubleshoot the issues.
1) Upon start-up, a folder with a question mark appears briefly, then is quickly replaced with the standard Apple logo. This process takes at least a minute or more from a cold boot-up.
2) When I log-out from another User account and try to log back into my User account, I can't. I must restart the comp to log back in. I checked the account directory and everything is the same. Don't know why I must reboot to log back in.
3) Occasionally when working in an app like iPhoto the system acts like it can't find my files, indicating it's confused where I keep my photos and stuff.
4) Shut downs take 3X longer than before. Again, as if the system is searching for things and can't figure out what's what.
I'll try to describe my set up (Mac Pro running Lion):
SSD: System/System Folder/Applications/Library/Resources/Users (random non-essential files in the folders)
HDD: System (nothing in it except Library/Cache with only "com.apple.bootstamps" in it)/Users (all Directories and user folders & files)/Desktop
Have I got things configured correctly? Something missing, something askew?
Thanks for any insights!

I'll try to describe my set up (Mac Pro running Lion):
SSD: System/System Folder/Applications/Library/Resources/Users (random non-essential files in the folders)
HDD: System (nothing in it except Library/Cache with only "com.apple.bootstamps" in it)/Users (all Directories and user folders & files)/Desktop
Have I got things configured correctly? Something missing, something askew?
What a mess!  I am not sure what you read because if what you showed is is really what you have it's a wonder you can run at all.
• SSD: System/System Folder/Applications/Library/Resources/Users (random non-essential files in the folders)
Users should be in /Users.
• HDD: System (nothing in it except Library/Cache with only "com.apple.bootstamps" in it)/Users (all Directories and user folders & files)/Desktop
There's probably a LOT more in there but you just cannot see them.
I thought your intent was to make the HDD contain your home dir and use the ssd as your boot dir.  What you describe on the surface appears you ended up trying to do the reverse (and doing it poorly).  I'm guessing you specified the ssd as your boot drive in System Preferences Startup Disk.  So when you boot the machine looks there, says "what the f**k?" (probably the question mark you see), and then finds a bootable system on your hdd.
I suggest you reread how to move a home directory.
How to Move the Home Folder in OS X – and Why
Moving your home folder in OS X

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