Hi James,
Sorry to hear what happened to you. But, it's often best to check with a computer expert before you start messing around with moving programs from one hard drive to the next. Bad things usually ensue.
Mike and Holdum gave you some good suggestions here which you may want to follow. You can check your Recycle Bin and attempt to restore the deleted systems files to your bootdrive (C: drive), but in my experience this usually fails, and you are looking at a Windows Reset almost certainly. You said you didn't mind doing it, but didn't want to. That's a Mixed Message I get on a daily basis on the forums I volunteer on. <grin>. Which is it? No one likes to do a complete rebuild, but when you do something catastrophic it's pretty much inevitable.
In regards to Mike's suggestion about installing all your programs onto the D: drive, and leaving C: drive with just the Windows system files and registry hive; I've got mixed feelings about that. It works for Mike, but doesn't work for everyone. There are thousands or tens of thousands of programs out there for Windows machines; however, not all of them take kindly to redirecting their install folders to a non-C: drive location (a secondary drive if you will). It's best to read the installation instructions if the program comes in a retail box with disc, otherwise you need to go to each FAQ on the website of each program you intend to redirect it's installation folder to. If you have 30 or 50 or 100 programs you are currently running on your machine, this can not only be time-consuming, it could lead you into a nervous breakdown. (I've had several from trying to do this for Clients over the years!
Mike has taken months or years to figure out which programs can be run this way, and he may have eliminated the ones he can't with other programs--that's not an easy process, I'm here to tell you. But, it's like a lot of advice we give here; what works well for one user may not work well for another. If you have the patience (as Mike clearly does) to do this, I suggest if you attempt to copy Mike's minimalist Windows install on your SSD bootdrive, when you install your programs onto your secondary hard drive (D: drive), that you do them one at a time, making sure to power-cycle your machine after each program installation. This will mitigate the possibility of overlapping memory leakage; a big problem on computers today and even worse in years gone by. You need to clear out the RAM and make sure that all entries into the Registry are completed for each program individually; as multiple installs can cause havoc in your various Memory Pools. This is tekkie talk for "no-Bueno". Power-cycling after each program install will help prevent this. Don't be surprised though that if you install 25 programs in the same day, you may come up with a Blue-Screen and have to troubleshoot that issue to find out which of the 25 programs is the culprit! Not a fun task, and very likely will require 1 or more Windows resets to accomplish a clean-running system. I'm not saying you shouldn't do it Mike's way, as it has some good advantages. It doesn't work for me, since I use many programs that Windows doesn't like running from a secondary drive location; and I know this, so I suffer through having to make large backup images (right now about 172GB each), and I need multiple external usb drives to store them on. It's quite a process.
Just some food for thought,
Best of luck,
<<<BIGBEARJEDI>>>