Asking for analysis

Install an older driver version and don't install CCC, just the basic driver.

Do you still have Driver Verifier enabled?

Add brand names to your system specs for hard drives, PSU, and any others.

Do you always have your external HDD connected?
Disconnect it and tell us if anything changes, leave it disconnected for testing purposes. You can connect it if needed, then disconnect it afterwards.

Which ports are your HDDs connected to?
Which SATA controller driver are you using?
Device Manager>IDE ATA/ATAPI contoller>Intel series - right click 'Properties' - Driver


System event log info.

Run HDD diagnostic utilities for all your hard drives.
Run ExcelStor ESTest – Drive Diagnostic test
Run Seagate SeaTools– Short Drive Self Test and Long Drive Self Test

Appears to be your ExcelStor HDD giving the errors.
Even if the ExcelStor HDD passes the diagnostic test, disconnect it for testing.

There are a lot of these.

Code:

 Event[13]:
  Log Name: System
  Source: Disk
  Date: 2011-07-17T17:44:07.837
  Event ID: 11
  Task: N/A
  Level: Error
  Opcode: N/A
  Keyword: Classic
  User: N/A
  User Name: N/A
  Computer: mpriki-PC
  Description: 
The driver detected a controller error on \Device\Harddisk2\DR2.

This crash blames a driver, could be a hardware fault and the driver is blamed due to using Driver Verifier.

Crash code: STOP 0x000000D1: DRIVER_IRQL_NOT_LESS_OR_EQUAL

Usual causes: Device driver
Cause:
A driver tried to access an address that is pageable (or that is completely invalid) while the IRQL was too high.
This bug check is usually caused by drivers that have used improper addresses.

Code:

Event[8441]:
  Log Name: System
  Source: Microsoft-Windows-WER-SystemErrorReporting
  Date: 2011-07-14T22:27:35.000
  Event ID: 1001
  Task: N/A
  Level: Error
  Opcode: N/A
  Keyword: Classic
  User: N/A
  User Name: N/A
  Computer: mpriki-PC
  Description: 
The computer has rebooted from a bugcheck.  The bugcheck was: 0x000000d1 (0x0000000000000000, 0x000000000000000b, 0x0000000000000000, 0xfffff88004959fdc). A dump was saved in: C:\Windows\MEMORY.DMP. Report Id: 071411-18844-01.

This is just the start of the diagnoses, let us know the results of the tests and details of the other recommendations.

When doing a long diag post I reply and continue to edit, this serves as a save function so the information isn't lost. It also takes some time doing the research.

Your attachment link doesn't work.
For posting the information , enter 'Snipping tool' in the Start button > Search box, hit enter. Select the area you want to post and save to a convenient place.
How to Post a Screenshot in Seven Forums

If the Excelstor won't run the diag test, might be due to it's age, or it is bad.
Not sure about running the SeaTools test on the Excelstor, the fact that it failed may or may not be relevant.

I've always had the SeaTools long test available, try re-burning the CD, slowest speed available.

Chances are if you had the Excelstor connected when you installed the new HDD and OS it took the boot files. This is usually the reason the system won't boot without another drive.

Disconnect the Excelstor, and all other HDDs except the one with the Win7 OS on it, and run Startup Repair minimum of three times with re-boots in between.
How to Run a Startup Repair in Windows 7

This will put the boot files on the right HDD.

Check in Disk management for which partition is marked 'Active', with the 40GB drive connected.
Best to post a snip of Disk Management, so we can have a look.

Did you re-boot after every startup repair?
It will actually perform the repairs on the re-boot, and can only do one major repair at a time, this is why you have to run it three times with re-boots after each repair run.

Check this tutorial: Startup Repair - Run 3 Separate Times

In Disk Management right click the external drive and mark as 'Inactive'.
Same thing for the Excelstor drive, mark as 'Inactive'.

If you have any problems doing this, or don't want to use DiskPart as in the tutorial.
Download: Free Partition Wizard

You can use the full version, the CD or USB version to easily do this.

Here are a couple of tutorials that explain what this utility can do, but it will also easily change the 'Active' designation.
Partition Wizard : Use the Bootable CD

The steps to change the 'Active' designation:
Open Partition Wizard (PW)
Select the Windows 7 partition, right click > Modify > Set Active.
Select the partition (Excelstor and then the external HDD) that is showing under the Status column "Active", right click > Modify > Set Inactive. Do this for each partition designated 'Active' except for the one you want to boot from, Windows 7.
Then click the large Green Check mark icon in the upper left corner labeled 'Apply'.

Then run Startup Repair three separate times with re-boots after each run.

For future reference, when installing an OS always dis-connect all other hard drives except the one you are installing to. Also make sure no other partitions are marked 'Active', and to be sure, mark the partition you are installing to 'Active' before you start the installation.
This method will give you a single boot OS. If you want to dual boot, you will need to leave the HDD/Partition with the older OS connected, the boot files will remain on the OS that was installed first.
This will work when installing a new version of OS while keeping an older version.
It doesn't work if you have Win7 installed and try to install Vista or XP. It can be done but is more difficult.