After clone, bootmgr is missing

So, I was running low on space on the primary boot drive on my desktop. So, I decided to get a larger drive and clone the existing boot drive to it in order to avoid the hassle of OS reinstall and reinstalling all the programs. I used EaseUS to do the clone, and it went just fine. I went into the disk manager and set the two new partitions as active, then shut the computer down and disconnected the old drive and connected the new drive to the same port as the old one, just to be safe as some MB ask for that.

This is where the problems began. On reboot, the system said that the BootMGR was missing. Not really all that uncommon, usually fixable by running startup repair from a repair disk, which is what I did. The odd thing was that when i ran the repair disk, no OS was listed to be repaired. I thought little of this as I figured it could be just not detected until i ran startup repair, which i did. However, the same error greeted me on restart "BootMGR is missing"

So, I shut the computer down, disconnected the new drive, reconnected the old drive, and restarted the computer, figuring something must have gone wrong with the clone that had not been indicated to me by EaseUS. And again, same error. Startup repair, same error. Running chkdsk now to see if it comes up with anything, but I doubt it will as the system was running fine on this drive earlier. I do not have access at the moment to an install disk for Win7 or I would try the repair install function on it, and I may still, but I would rather not wait until Monday when I will be able to get a disc.

What i have tried
Startup repair several times
using diskpart to deactivate all volumes, then reactivate just the main OS volume and the system reserved volume
There was some odd drive letter assignment going on, so I used diskpart to return that to the way that it was

Kinda at wits end here. An thoughts would most certainly be appreciated.

Drive letter assignment shouldn't matter, as Windows reassigns on boot.
How did you set more than one partition on the same disk as Active? That's not possible.
IME, the Repair Enviro doesn't handle missing bootmgr's automatically well. You need to open a command window and do it manually.
But if it's not even seeing the OS at this point, and if setting the proper partition to Active doesn't remedy that, maybe a new clone would be simplest.

Well, thankfully, my presumption was wrong. chkdsk did find some errors and fixed them, so the system was able to boot up with the old drive. I think I am going to do a sector by sector clone this time to the new drive and see if I can get it up and running that way. If not, it will be doing chkdsk on the new drive and see if that fixes problems with it like it did for the old one.