New SSD,wonky boot up

Greetings,
I just installed my new SSD(Vertex4) and cloned with using Clonezilla. I performed disk to disk image and also moved the MBR over as well to the SSD. After following the instructions listed by HTG(How To Migrate Windows 7 to a Solid State Drive - How-To Geek)I'm finding that I'm having issues with booting. I performed a couple of restarts after a successful completion to verify everything was in working order(and check out those new sweet boot up times); everything was working fine. I shut down,and came back,now I'm getting Missing OS and MBR not found issues. Also,since my HDD is 500GB and the SSD is 512, I seem to have an 11GB partition thats just sitting around doing nothing. How to resolve this?

Thanks in advance.

Make sure the 100mb System Reserved (preferred if you have it) or C partition is marked Active first: Partition - Mark as Active (Method Two)

Then

Ztruker said:

Run Startup Repair, up to 3 times. That should resolve the problem.

I am now booting off the SSD without any issue. However, I noticed the the 100MB System Reserved Partition is on one of my storage drives and not on the C drive. Shouldn't it be on the C drive?

Enclosure.

This is because you didn't unplug all other HD's when installing to C. To correct it mark all Active partitions Inactive: Partition - Mark as Inactive - Windows 7 Forums

Then mark C Active: Partition - Mark as Active

Power down to unplug all other HD's, reboot to confirm in BIOS setup that C HD is set HD first to boot. Boot into Win7 installer or System Repair Disk to run Startup Repair - Run up to 3 Separate Times.

The System Reserved Partition is still located on the 1TB HDD. Went through all of the steps.

Enclosure.

Yes but C is now being booting itself as signified by the System Active Boot flags. So your problem is solved.

You'll notice System flag has now been removed from System Reserved, which means you can go ahead and delete it, resize into the space if you want using Partition Wizard Resize Partition - Video Help.