Will reinstalling OS X from scratch tidy up problems?

Hello,
I'm guessing that normally the answer to my question would be yes. However. I bought my 15" MacBook Pro just over a year ago, and having little experience with macs kind of made a mess of it while checking out as many free apps (many of which I removed) as possible before deciding I was better buying apps that had good reviews - a decision that has worked out well. However, this was after some 'damage' was done. Early on I noticed that the computer would not shut down properly, so I did a hard reset a few times. It shut down and booted up after that, but slower than originally. It can take between 30 seconds to a minute to start up now. I upgrade to Mountain Lion shortly after its release, a decision which I don't regret, but start up times have not improved. I keep a full time machine backup of the whole computer. What I'm wondering is, if I make a fresh reinstall of the OS and then restore from Time Machine, will all the left over junk and the slow start up etc be restored to it as well? Or, will the system run better despite everything being restored from Time Machine?
Thanks and blessings,
David.

It may depending upon what the issues are. In your case, howwver, reinstalling from scratch then restoring your Time Machine backup will simply restore whatever was causing problems before. The only way to avoid such issues is to reinstall from scratch, but not restore anything from your Time Machine backup. Reinstall what you need from their various sources such as re-downloading or installing from DVD media. Only install one item at a time, then test for a while to be sure you don't have any problems. Verify compatibility before you install any software - App Compatibility Table - RoaringApps - App compatibility and feature support for OS X & iOS.
Install or Reinstall Lion/Mountain Lion from Scratch
Be sure you backup your files to an external drive or second internal drive because the following procedure will remove everything from the hard drive.
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
Erase the hard drive:
1. Select Disk Utility from the main menu and click on the Continue button.
2. After DU loads select your startup volume (usually Macintosh HD) from the
      left side list. Click on the Erase tab in the DU main window.
3. Set the format type to Mac OS Extended (Journaled.) Optionally, click on
        the Security button and set the Zero Data option to one-pass. Click on
      the Erase button and wait until the process has completed.
4. Quit DU and return to the main menu.
Reinstall Lion: Select Reinstall Lion/Mountain Lion and click on the Install button.
Note: You will need an active Internet connection. I suggest using Ethernet if possible
            because it is three times faster than wireless.

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