Strange Application Issues after Mountain Lion Upgrade!

Question

I'm having, what I believe to be, strange issues with a clean install of Mountain Lion from 10.6.8
It's for my boss' computer at work so I can't afford to have it down for very long at a time. It's hard to pinpoint the issue(s).
Computer:
Mac Pro - Early 2009
OS X 10.8.3
2 x 2.6 GHz Quad-Core Intel Xeon
32 GB 1066 MHz DDR3
The startup disk is 4x2TB RAID 5 using Apple RAID card (Firmware version: E-1.3.2.0; Hardware Revision: 2.00; Driver version: 124
The following is what happened/is happening:
1. (Tuesday)
Created a bootable backup of system drive using Disk Utility
Performed a Clean install
Used migration assistant to copy over applications from backup
Downloaded (from Amazon) and installed Microsoft Office 2011
Imported Addresses (including imported Previous Recipients that were imported into Contacts before exporting on old system)
Setup email & copied over mailboxes from backup
Moved all files back onto the system (User folders)
Everything worked fine from Wednesday - Sunday.
Problems reported to me (Sunday)
"Chinese characters" on save dialogue box in Microsoft Excel
Mail crashed while dragging a photo from safari to it
After a restart, Mail, all Microsoft Office apps, and Final Cut Pro wouldn't open.
Tried to reset preference files, but nothing worked.
2. (Monday night)
Performed another Clean Install
Migrated Applications
Transferred mailboxes (not old emails at this time)
Imported same group of addresses as before into Contacts
Installed Microsoft Office
Moved user data back
Transferred old email mailboxes (Tuesday afternoon)
Everything worked fine Tuesday - Thursday early morning)
Problems reported to me (Thursday morning)
When typing in an email address to send an email, it didn't autofill. Mail crashed.
Mail wouldn't open. Different from last, this time it said the ~/Library/Mail folder was moved. I checked and the folder was there with everything in it fine.
The Microsoft applications that were open at the time of the Mail crash still worked, but others wouldn't open. After closing the open applications then they wouldn't open back up (same as before)
Final Cut Pro opened fine.
Fixed Mail by deleting the ~/Library/Containers/com.apple.mail folder.
Later found out that though Final Cut would open it would crash when loading a project and that Quicklook wouldn't work for quicktime files across the network & codecs were missing (this could have been cause by me when trying to test problems).
3. (Sunday)
Restored from a different bootable backup I made after 2nd clean install and migrated applications.
Repaired Permissions using Disk Utility
Moved over Mail data
Copied over user data
*Didn't import the addresses
Checked to make sure all the fonts were validated and no duplicates
Everything worked fine after install and through Monday.
Problems to me (Tuesday morning)
Microsoft Office disappeared completely from the computer. No folder in Applications or dock icons.
Slower to connect to network files
Re-installed Microsoft Office to keep work progress going.
What would be causing this peculiarity? It works after I fix it and for a little afterwards but then strange things happen.
Would repairing disk permissions on bootable backup (of 10.6.8) before using migration assistant help?
What is the best way to track down what is causing these issues?
Thanks!

Answer 1

I suggest that the best way to upgrade from 10.6.8 to Mountain Lion is one of the following:
(1) Simply perform an upgrade install. This is in fact Apple's recommended approach. I am not sure why you have not yet tried that. I have done this myself successfully.
(2) Make a backup of the working 10.6.8 system; better yet is to make two complete backups, one being a "clone," the other being a Time Machine backup. Use of two different methods gives you options should something go wrong. Then erase the original disk and install Mountain Lion, and on the first boot up run Setup Assistant (which is better than Migration Assistant) and transfer over EVERYTHING, including user accounts, settings, applications. I have also used this approach, also successfully.
You did neither (1) nor (2), but seem to have done some sort of hybrid by transfering applications and then manually moving over some mail files and moving over some user files. I don't think this is a recommended approach. It can result in permissions issues, which can cause things to "disappear" or otherwise behavior oddly.
I do not understand how your use of a RAID setup and a RAID card might affect any procedures which otherwise might work smoothly. Are you 100% certain that your RAID hardware and firmware are compatible with Mountain Lion?
Assuming that the RAID is not the issue and it behaves to the OS just like a normal disk, I would try the full disk erase and install of Mountain Lion followed by a Setup Assistant on first boot up to move over everything from your clone backup.
If this does not work, then I would erase and restore back from your clone, so you get your 10.6.8 system working again. Then I would try a simple upgrade install of Mountain Lion.
If that fails, then I would erase and install Mountain Lion with one new administrative user created who has a different user name than the person whose stuff you need to restore. Then with that new administrative user I would make sure the RAID is all up and running. Then I would use Migration Assistant to migrate over users only and would reinstall all software from scratch. If that is not to your liking, I'd as a less desirable alternative use Migration Assistant to migrate over everything, applications and users. You will have that new, extra administrative user as well as the original user(s), but that should cause no harm.