Yes you can. I did basically that last night but it was on a separate partition on the internal drive and again today on an external drive. I did save the downloaded ML install files and use the latest version of this software to create a ML Install USB thumb drive.
Used the thumb drive I created to do the install on the external.
No a Clean install is just that, A clean install. No programs will be installed or carried over. You can use the original disk to migrate your data over. That is what I did. Once the install if finish the system will reboot to the basic setup screens. Country language selection and one of them will be something like, "Would you like to import/migrate/whatever your data from an older Mac, time Machine backup or Disk. I selected Disk as I installed ML on the same physical disk, just into another partition. I then selected the disk to use and clicked OK or Apply and off it went. When it was done all my files, settings and programs were Copied over and I have a complete working system.
I feel this is a better way of doing a upgrade of the OS instead of installing On Top of the original OS. But I may be wrong in that.
Once you have the new drive and the SATA docking station insert the new drive in it and connect it to the Mac.
Open Disk utility, found in the Utilities folder in your Applications folder, and click on the Drive name, Or the Docking stations name (As sometimes the drive name really isn't seen. Just the name of the docking station) in the left hand part of that windows and click the Partition tab. Select One partition from the drop down in the center of that window, Partition Layout area. In the name field name it what ever you like, you can even call it Macintosh HD if you like (it is just a name), and select Mac Extended (Journaled) from the drop down in the Format area (Just below the name area). At the bottom of the Partition section (The center section of the window) there is a Button labeled Options. Click that and select GUID as the Partition Table. Close that Options window/screen and then select Apply. Once that is finshed close down Disk utility.
Now open the Mac App store link in the dock and select Mountain Lion and buy it. It will start to download and when it is finished downloading a window will open up on your desktop. Once that Window open do NOT Click Anything on that Window. Open a Finder window and look in your Applications folder. You should see a file name Install OSX Mountain Lion.app, highlight that by clciking on it once and press the Command+c keys, that will copy it. Highlight your current internal Macintosh HD and then press the Command+v keys. That will paste a copy of that file into the ROOT of the Macintosh HD.
Now once that has finshed copying that file you can close the Finder window and you should be back at the Install Mountain Lion window (if not it is in you dock. click on it the window will re-open) Now select Continue and at some point you will get a screen to Select which drive to install Mountian Lion to. Select the external drive/docking station you just partitioned and formatted in Disk utility (it will be market with a USB symbol If it is a USB docking station. If not a USB docking station then whatever connection type it is will have a different icon symbol then the internal drive) as the install location. Click Continue again and from there you may get some License screens and an Agree button and then an Agree drop down from the top of the screen. Click the OK/Agree/Continue button on all of them. At that point the install files will be copied to the external drive with a Time Remaining bar. Once that has finished copying the install file to the external the system will reboot and the install will start. Once that is done the system will reboot again and you will be at the Mountain Lion User Setup screens.
From there you will get a screen to migrate/import from your current system and then you must select Disk and then your intrernal Macintosh HD partition. Once that is done you are finished and the drives can be switched out.
You may want to copy and paste all this into a text document and print it out.
Good Luck and best wishes.