YOUR SSD DRIVE MAY BE INCOMPATIBLE WITH YOUR MOTHERBOARD
Before we dive into the waters of that terrifying statement, lets eliminate some of the basics.
First of all, you shouldn't be trying to repair a cloned drive. If the source drive was in good working condition, the clone should come out the same. If the source drive was defective, that's a different story. To correct your problem you need to go back to the clone and get it right.
1. Make sure both your bios and SSD drive have updated firmware.
I know this sentence is annoying, but it may be the difference maker here. Most SSD manufacturers are releasing firmware updates to battle a huge plethora of issues and incompatibilities that are arising as SSD drives become mainstream. The firmware update will erase all your data, so it needs to be done pre-clone.
2. Try new SATA cables and ports
When I say this I don't mean to just plug the drive into a new cable and hope it boots, I mean do your clone again with new or different cables and switch up the ports. Motherboards often supply extra SATA ports with additional features, that may cause problems, or a particular port may be defective. If the SSD is your C: drive, it's good practice to have it on port 0 or 1.
3. Try erasing the drive and initializing it before you clone
When I say erasing, I don't mean formatting, you should do a sector by sector wipe of the drive. There are many freeware applications to perform this, such as Active KillDisk. Once this is done, initialize the disk to match the source drive, whether it be MBR or GPT, make sure it is the same. Now try your clone again. Hiren's Boot CD has everything you need for this.
4. Try different cloning software
I personally have had scenarios where one piece of software creates a drive that won't boot and another does a perfect clone, and vice versa with the same software. One would assume, that different software is using different methods of transfering/migrating the data. It also seems to be based on which particular SSD drive you are using. I personally prefer to use Acronis True Image 2015 (not free) for this type of stuff. You can erase the disk, initialize it, and clone, all in a bootable suite that supports SSDs.
5.Try your clone in a different PC
This one is self explanatory. Once the clone is done, put the drive back into the PC it's intended for. Cross your fingers as it attempts to boot into windows. You may have some luck after all!
If you have exhausted all these resources, you may have an SSD / mobo incompatiblilty and there are only two ways to solve that... The fact that yours is not recognized in the bios is a key indication that there may be a disagreement. One of the most common feuds is Sandforce controllers vs Nvidia chipsets. Do some research and see what you can find, keep in mind though that SSDs have just recently become common hardware, so you might not find exactly what you're looking for. The best way to be certain of this, is to contact your SSD manufacturer. They will be able to tell you if your ssd is compatible with the rest of your hardware. If it isn't, you should be able to sell it for near market value to someone with a compatible system.
You may be able to get around an incompatibility with a PCI-express sata card. Some people have had success with this. I'm not sure how stable it is or how it will effect read/write speeds, but it may be an affordable workaround.