Mac Pro 5,1 Freezes & Pinwheels at Boot, Corrupt Font to Blame?

Question

Hello, all. This is my first post on the Apple Support communities as I have a very strange issue that seems to be nowhere else on the Internet, so I'll ask it here before running off to my local Genius Bar.
I'm running a Mac Pro Mid 2010, with a 2.8 GHz Quad-Core Xeon and 16GB DDR3 RAM. The only aftermarket/third-party component I have installed is a Blackmagic Intensity Pro internal video capture device, which, to my knowledge, works perfectly.
I am currently typing this on my third re-install of Mountain Lion, as I have not been able to advance to the login screen after I boot my Mac Pro, due to freezing and the spinning pinwheel.
I may have an idea what's causing this issue, but I'm not sure how to pinpoint it, remove it or figure out what to do. It may be tied to a conflicting Geneva font, located in (my name) > Library > Fonts. This is not the "True" Geneva font, as that is located in the System > Library > Fonts folder on my primary hard drive. This "impostor" Geneva has a ".ttf" file extension while the original Geneva's extension is .dfont.
Here's an image of the window that pops up:
Before the problem happened (and before the boot freezing happened), I selected "Move To Trash" and thought nothing of it, seeing as though it's a fairly standard warning message.
On my first re-installation, I selected "Move To Trash". I did not see the font in the trash but had other files there and securely emptied it. I rebooted shortly afterward and the system locked up/pinwheeled before the login screen. On my second re-installation, I selected "Ignore Conflict" but I ended up with the same result. Notice the impostor "Geneva" seems to have a lock near its filename. Maybe this is what's holding it up.
The only other common message OSX gives me on each installation is a prompt to install a Java SE 6 Runtime, but it seems to be through the standard Apple Software Update so I doubt it's anything that would corrupt an installation.
These font conflicts stem from fonts that I transferred over from my old PC when I first bought my Mac Pro after Christmas in 2010. No issues have surfaced until now other than minor aesthetic issues that were easily resolved.
Now, I'm left with a dilemma (which is what brought me here). I need to find a way to resolve this, as I think this issue may be what's holding my computer up. I've done research and found that tampering with system fonts will cause your Mac to crash at startup. I'm a freelance video producer so this has been causing me more than a few headaches when attempting to do my work, so I'm scurrying for a result ASAP.
I've tried nearly every method of fixing the issue...repairing my boot disk, verifying/repairing permissions, resetting my password and resolving ACL conflicts,  unsuccessfully trying Safe Mode, resetting PRAM and now re-installing Mac OSX. This is most likely an issue on the OS end --- my hardware is working properly, its S.M.A.R.T. status is verified, and permission/disk repair/verify shows no errors. I also have a Boot Camp partition that runs flawlessly --- I can even access folders and files on my Mac from the Windows parition, so it's probably not an issue of a dying hard drive. There's something screwy preventing me from logging in, and short of the first boot after re-installing Mountain Lion, there hasn't been a way to log in normally.
I'd rather not reformat my entire startup drive because of what could be one file conflict, as I have a lot of personal data and presets I'd like to keep. Nevertheless, I have an appointment at my Apple Store's Genius Bar set up for Friday but I'm leaving it as a worst-case scenario as I'd much rather pinpoint these issues myself.
If you've made it this far, thank you for reading this long post. I wanted to be as specific as possible regarding the strange issues happening with my Mac Pro. Hopefully someone has a suggestion out there that doesn't involve reformatting as I'm 90% sure this boot error has to deal with this system font conflict. The other 10% wonders what needs to be done.
Thanks in advance!

Answer 1

First check that you still can't boot as usual. If you can't, see below.
Please read this whole message before doing anything.
This procedure is a diagnostic test. It changes nothing, and therefore will not, in itself, solve your problem.
Third-party system modifications are a common cause of usability problems. By a “system modification,” I mean software that affects the operation of other software — potentially for the worse. The procedure will help identify which such modifications you've installed, as well as certain other aspects of the configuration that may have a bearing on the problem. Don’t be alarmed by the apparent complexity of these instructions — they’re easy to carry out and won’t change anything on your Mac. 
These steps are to be taken while booted in “normal” mode, not in safe mode, if possible. If you’re now running in safe mode, reboot as usual before continuing. If you can only boot in safe mode, you can still use this procedure, but not all of it will work. Be sure to mention that in your reply, if you haven't already done so. 
Below are instructions to enter UNIX shell commands. The commands are safe and do nothing but produce human-readable text output, but they must be entered exactly as given in order to work. If you have doubts about the safety of the procedure suggested here, search this site for other discussions in which it’s been followed without any report of ill effects. I am not asking you to trust me. If you can't satisfy yourself that these instructions are safe, don't follow them.
The commands will line-wrap or scroll in your browser, but each one is really just a single long line, all of which must be selected. You can accomplish this easily by triple-clicking anywhere in the line. The whole line will highlight, and you can then copy it.
Note: If you have more than one user account, Step 2 must be taken as an administrator. Ordinarily that would be the user created automatically when you booted the system for the first time. Step 1 should be taken as the user who has the problem, if different. Most personal Macs have only one user, and in that case this paragraph doesn’t apply.
Launch the Terminal application in any of the following ways: 
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.) 
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens. 
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid. 
When you launch Terminal, a text window will open with a line already in it, ending either in a dollar sign (“$”) or a percent sign (“%”). If you get the percent sign, enter “sh” and press return. You should then get a new line ending in a dollar sign. 
Step 1 
Triple-click anywhere in the line of text below on this page to select it:
PB="/u*/*/Pl* -c Print"; { echo Loaded kernel extensions:; kextstat -kl | awk '!/com\.apple/{printf "%s %s\n", $6, $7}'; echo $'\nLoaded user agents:'; launchctl list | sed 1d | awk '!/0x|com\.apple|org\.(x|openbsd)|\.[0-9]+$/{print $3}'; echo $'\nInserted libraries:'; launchctl getenv DYLD_INSERT_LIBRARIES; echo $'\nUser cron tasks:'; crontab -l; echo $'\nGlobal launchd configuration:'; cat /e*/lau*; echo $'\nPer-user launchd configuration:'; cat .lau*; echo $'\nGlobal login items:'; $PB /L*/P*/loginwindow.plist | awk -F'= ' '/Path/{print $2}'; echo $'\nPer-user login items:'; $PB L*/P*/com.apple.loginitems.plist | awk -F'= ' '/Path/{print $2}'; echo $'\nSafari extensions:'; $PB L*/Saf*/*/E*.plist | awk -F'= ' '/Bundl/{print $2}' | sed 's/\..*$//;s/-[1-9]$//'; printf "\nRestricted user files: %s\n" $(find ~ $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 \) | wc -l); echo $'\nExtrinsic loadable bundles:'; cd; find -L /S*/L*/E* {,/}L*/{Ad,Compon,Ex,In,Keyb,Mail/Bu,P*P,Qu,Scripti,Servi,Spo}* -type d -name Contents -prune | while read d; do /usr/libexec/PlistBuddy -c 'Print :CFBundleIdentifier' "$d/Info.plist" | egrep -qv "^com\.apple\.[^x]|Accusys|ArcMSR|ATTO|HDPro|HighPoint|driver\.stex|hp-fax|JMicron|print|SoftRAID" && echo ${d%/Contents}; done; echo $'\nUnsigned shared libraries:'; find /u*/{,*/}lib -type f -exec sh -c 'file -b $1 | grep -qw shared && ! codesign -v $1' {} {} \; -print; echo; ls -A {,/}L*/{La,Priv,Sta}* L*/Fonts; } 2> /dev/null | open -ef
Copy the selected text to the Clipboard by pressing the key combination command-C. Then click anywhere in the Terminal window and paste (command-V). I've tested these instructions only with the Safari web browser. If you use another browser, you may have to press the return key after pasting.
The command may take up to a few minutes to run, depending on how many files you have and the speed of the computer. A TextEdit window will open with the output. Post the contents of the TextEdit window (not the Terminal window) — the text, please, not a screenshot. You can then close the TextEdit window. The title of the window doesn't matter, and you don't need to post that. No typing is involved in this step.
Step 2 
Remember that you must be logged in as an administrator for this step. Do as in Step 1 with this line:
{ echo "Loaded system agents:"; sudo launchctl list | sed 1d | awk '!/0x|com\.(apple|openssh|vix\.cron)|org\.(amav|apac|cups|isc|ntp|postf|x)/{print $3}'; echo $'\n'"Login hook:"; sudo defaults read com.apple.loginwindow LoginHook; echo $'\n'"Root cron tasks:"; sudo crontab -l; echo $'\n'"Log check:"; syslog -k Sender kernel -k Message CReq 'GPU |hfs: Ru|I/O e|find tok|n Cause: -|NVDA\(|pagin|timed? ?o' | tail | awk '/:/{$4=""; print}'; } 2> /dev/null | open -ef
This time you'll be prompted for your login password, which you do have to type. Nothing will be displayed when you type it. Type it carefully and then press return. You may get a one-time warning to be careful. Heed that warning, but don't post it. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
You can then quit Terminal.
To prevent confusion, I'll repeat: When you type your password in the Terminal window, you won't see what you're typing.
Note: If you don’t have a login password, set one before taking Step 2. If that’s not possible, skip the step.
Important: If any personal information, such as your name or email address, appears in the output of these commands, anonymize it before posting. Usually that won't be necessary.
Remember, Steps 1 and 2 are all copy-and-paste — no typing, except your password. Also remember to post the output as text, not as a screenshot.
Please post the contents of the TextEdit window, not the Terminal window.