Reformat iMac 2007

I have a 2007 iMac that had the hard drive replaced, operating system reinstalled and worked great. However something happen and some stuff became missing on the system. I reinstalled the system using the orginal disk and Snow Leopad and upgraded back to the current OS. Since I have reinstalled the system, I have a lot of issues with closing Safari, Finder and others that are open. I have a box that pops up after a while and ask me to force close programs and to relaunch Finder. In the box it says something about not enough space on the disk, something to that effect. It's obvious I did not reinstall the system properly, what is the proper way of reinstalling the system? Started with Leopard, then Snow Leopard and downloaded Mountain Lion from the app store which worked great before I had some stuff come up missing.
I have a 1TB hard drive and 4G of memory.

Sounds like there are a couple of things wrong.
1. When you erased and formatted the Hard Drive yourself using your Install or Upgrade DVD, did you return the drive back to 1 Partition in the Partitioning step...?
2. Not all, but many of your older 06' or 08' iLife App's from Tiger or Leopard will not run in Lion and will need to be purchased from the App Store.
The "not enough disk space" is a real problem and I would backup to an External HD if you have not already done so and start over from the beginning.
First off, exactly which Install Disc's do you have, because originally that iMac came with Tiger 10.4.10 and an Additional Software Disc set. Which means that both Leopard and Snow Leopard can only be upgraded using a Retail Upgrade DVD.
Second, if you are going to Lion (which is pushing that iMac) it might be better to Erase, Partition and Format using your white Snow Leopard Upgrade DVD, then upgrade to Lion and purchase newer versions of the iLife App's that you use. Besides you can always go back to your original Additional Software disc and get the older iLife App's that will still run in Lion.
To reinstall OS X from your original Disc set or a Retail Leopard / Snow Leopard Upgrade DVD
1. Boot from your original install disc set or uprade DVD and open Disk Utility.
2. Highlight the new HD in the list of drives and select the Partition tab.
3. Under Volume Scheme select 1 Partition and click on the Options... button.
4. Select GUID Partition Table in the drop down window and click OK.
5. Set the Format to Mac OS Extended (Journaled) and click the Apply button.
6. Then do a clean Install from your original Disc set or Upgrade DVD.

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