Am I doing something wrong or are these bugs?

Question

Hi All,
I have migrated my Mac from a MacPro 1,1 to a MacMini 6,2 with fusion drive. My other 4 drives are connected using a USB3 4-bay enclosure. 16GB RAM. The system is ML 10.8.2. I have run Onyx recently, but only cleared out those things that should be safe to work on (caches, monthly maintenance, etc). I have not run any MacCleaner type software.
These are some of the symptoms I am regularly having, maybe you guys can help?
Mail:
Having real trouble receiving mail from iCloud. Sending is OK I think.
Passwords for icloud accounts don't seem to verify, and when I click OK, I often get the beachball locking the whole mail app.
When amending/checking account detials in the preferences, the order of the mailboxes in the tray changes. (is this normal?)
Finder:
I have re-applied a new command (new email with selection ⌃⌥⌘N) but it does not work at all. It did in Lion.
Certain USB drives are showing up in the Sidebar that shouldn't be. Even when I remove them from the Sidebar they return.
TimeMachine:
Fails at least once a day, usually compaining that it cannot create a folder. I have followed the instructions faithfully here: http://pondini.org/TM/C10.html But this does not fix things sadly.
Overall:
Semi-general wierd feeling of inertia/sluggishness (maybe I expect more from a brand new system?). I don't know if this is to do with the fusion drive learning what to put onto the SSD? But I only have 165GB on disk, and I am trying to keep that number below 128GB.
Apps like Photoshop and indesign take a lot longer to open up than even a colleagues MacPro 1,1 with LESS RAM and a crucial SSD drive.
Can you tell me if this could (realistically) have anything to do with Migrating the system rather than starting completely fresh? It's essentially the same system I have been using since 2007, and maybe before. If this is the case, what would you recommend to help clear out the cobwebs?
Thanks for your attention and help,
Aaron

Answer 1

Back up all data. Don't continue unless you're sure you can restore from a backup, even if you're unable to log in.
This procedure will unlock all your user files (not system files) and reset their ownership and access-control lists to the default. If you've set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it.
Step 1
If you have more than one user account, and the one in question is not an administrator account, then temporarily promote it to administrator status in the Users & Groups preference pane. To do that, unlock the preference pane using the credentials of an administrator, check the box marked Allow user to administer this computer, then reboot. You can demote the problem account back to standard status when this step has been completed.
Triple-click the following line to select it. Copy the selected text to the Clipboard (command-C):
{ sudo chflags -R nouchg,nouappnd ~ $TMPDIR.. ; sudo chown -Rh $UID:staff ~ $_ ; sudo chmod -R u+rwX ~ $_ ; chmod -R -N ~ $_ ; } 2> /dev/null
Paste into the Terminal window (command-V). You'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command will take a noticeable amount of time to run. Wait for a new line ending in a dollar sign (“$”) to appear, then quit Terminal.
Step 2 (optional)
Step 1 should give you usable permissions in your home folder. This step will restore special attributes set by OS X on some user folders to protect them from unintended deletion or renaming. You can skip this step if you don't consider that protection to be necessary, and if everything is working as expected after step 1.
Boot into Recovery by holding down the key combination command-R at startup. Release the keys when you see a gray screen with a spinning dial.
When the OS X Utilities screen appears, select
Utilities ▹ Terminal
from the menu bar. A Terminal window will open.
In the Terminal window, type this:
res
Press the tab key. The partial command you typed will automatically be completed to this:
resetpassword
Press return. A Reset Password window will open. You’re not  going to reset a password.
Select your boot volume ("Macintosh HD," unless you gave it a different name) if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select
 ▹ Restart
from the menu bar.