Well you didn't give enough information to know where you were in the process.
If your external clone boots OK, then replace the old drive with the new one. Boot from the external drive. Prep the new drive as follows:
Extended Hard Drive Preparation
1. Open Disk Utility in your Utilities folder.
2. After DU loads select your hard drive (this is the entry with the mfgr.'s ID and size) from the left side list. Note the SMART status of the drive in DU's status area. If it does not say "Verified" then the drive is failing or has failed and will need replacing.
SMART info will not be reported on external drives. Otherwise, click on the
Partition tab in the DU main window.
3. Set the number of partitions from the drop down menu to one. Set the format type to Mac OS Extended (Journaled.) Click on the
Options button, set the partition scheme to GUID (only required for Intel Macs) then click on the
OK button. Click on the
Partition button and wait the process has completed.
4. Select the volume you just created (this is the sub-entry under the drive entry) from the left side list. Click on the
Erase tab in the DU main window.
5. Set the format type to Mac OS Extended (Journaled.) Click on the
Options button, check the button for Zero Data and click on
OK to return to the Erase window.
6. Click on the
Erase button. The format process can take up to several hours depending upon the drive size.
Restore your clone to the new drive. Open Startup Disk and select the new drive as the startup volume and click on the Restart button.
Once the computer has started successfully from the new drive open Boot Camp Assistant and create your Windows partition. Install Windows then restore you Windows data/files backup.
You will need to use the Parallels uninstaller to uninstall Parallels. Then track down all related files and folders used by Parallels and delete them. Download Easy Find -
VersionTracker or
MacUpdate - and use it to locate all the Parallels related items. Then reinstall Parallels from scratch.