All was well until 10.7 + MAMP + xCode. Now...misery. Why?

Question

I'm a port from the PC universe. Been loving my iMac since 10.6 for about 2 years now. Recently, I decided to stop programming on the PC and move to the Mac and open source, namely PHP to start. That mean installing MAMP. No harm. Then, I entered the world of debuggin PHP without a debugger. Not fun. So, I joined the installed xDebug. Whoa! Problems all over. Issues Galore. Addressed the issues, joined the $99 developer community, downloaded xCode (for the compiler), upgraded to 10.7 Lion and fixed all sorts of stuff: paths, ini files, got pear working, php-config, phpize, xdebug.so extension.
Now that xdebug works, I downloaded JetBrains PHPStorm for my debugger along with Dreamweaver CS4 that I've owned all along. All should be well and good, but not so.
1. All of my Adobe CS products went to ****. I had to re-install and lost 2 yrs worth of customizations, plug-ins etc. That was Adobe's best suggestion.
2. My external disk drives locked up, there were now permission issues on all, but my internal drive, so I couldn't get to my Time Machine backups. In any case, I had changed so much I'm not sure it would have helped.
3. Reformatted all external drives. Lost all, but nothing there was that precious. One drive is a scratch disk, the other was my backups. I immediately made another TM backup. All went well after re-format.
4. Download OS X.7.3....Whoa, more issues. Mainly permissions. Adobe went to **** again, but I'd already lost everything that mattered, so I trudged through the permissions thing (Library and System seemed to be the primary offenders here). User System now exists everywhere and user "Me" is gone, as is user "Administrators" group. Tried getting rid of user system. Bad, bad idea. Started over, then just tried to add Me and Administrators group. Worked out.
5. Reinstalled Adobe a 2nd time.
6. Now, some of my drivers, namely HP Scanjet aren't working, download, reinstall, fix that.
7. Reinstalling HP drivers mucked up permissions again and I get all these Library permission issues on bootup. Fixed that for the 3rd or 4th time now.
There's more, but you get the idea. All I wanted to do in the beginning was use PHP 5.3 and be able to debug it. Now I have a "hard way" degree in debugging, Unix, and the mac OS. And, I still don't know what I've done wrong.
This permissions issue keeps cropping up. I've done the Verify/Repair Permissions thing a few times, same for the hard drive. doesn't seem to have an noticible effect.
Is there some sort of utility out there (or already here) that will help me get my machine stable once again. I've logged probably 40 hours doing the above and this is darn near reminding me of my life with a PC--but I had 30 years of driving that crate, so it wasn't as frustrating.
It's all about permissions and my user being installed, or not, in various locations that I'm guessing it used to be installed in. Plus, it seems RW permissions have changed to R. I've used Terminal to fix some of this along the way, and get all working correctly, but I'm scared now to turn off the darn machine, or to upgrade "anything" on it.
Advice is welcome.
Regards and thanks to all.
Dan
PS: Crap, I see a 10.7.4 on the OS dropdown. I could have gone all night without seeing that!

Answer 1

It sounds like you're randomly setting file permissions without any idea of what they should be. In nearly all cases, they should be whatever the software installer makes them. On very rare occasions, it may be necessary to repair the permissions of system files after running a defective third-party installer. It's certainly necessary if you've "mucked up" those permissions yourself. You may have mucked them up so badly that they can no longer be repaired in the usual way. In that case, boot from your recovery partition (command-R at startup) and run Disk Utility. That, at least, is safe from being mucked up, but it won't fix everything; only Mac OS system files.
If a third-party product doesn't work, reinstall it, and resist the temptation to change the permissions. If it still doesn't work, contact the developer for support.
Repairing the permissions of a home folder in Lion is a complicated procedure. I don’t know of a simpler one that always works.
Back up all data now. Before proceeding, you must be sure you can restore your system to its present state
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 page that opens.
Drag or copy — do not type — the following line into the Terminal window, then press return:
chmod -R -N ~
The command will take a noticeable amount of time to run. When a new line ending in a dollar sign ($) appears below what you entered, it’s done. You may see a few error messages about an “invalid argument” while the command is running. You can ignore those. If you get an error message with the words “Permission denied,” enter this:
sudo !!
You'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning not to screw up.
Next, boot from your recovery partition 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 recovery desktop appears, select Utilities ▹ Terminal from the menu bar.
In the Terminal window, enter “resetpassword” (without the quotes) and press return. A Reset Password window opens. You’re not going to reset the password.
Select your boot volume 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.