Major Headaches--nothing is "clickable" in Vista Home Premium 64, except in Safe Mode

The HDD had suffered from a firmware bug that caused it to not awaken from Sleep Mode.
The bug was corrected, but now Windows will only run in Safe Mode.
I think that the problem may have occured because I wanted to immediately clone the HDD to prevent my data from being lost for good.
Instead of putting the HDD into the original computer, I installed in in another identical model computer which has a software program installed that allows me to clone drives.
I had overlooked the fact that the HDD was going to have to recover from not coming out of sleep mode before being "shut off".
I turned the computer on and the computer booted from the repaired drive, instead of its own C drive. The HDDs are the same model.
Next, the computer launched Checkdisk and then it ran a Startup Repair, before I noticed what was happening.
In the end, I ended up with 1 HDD that won't function outside of Safe Mode and the other one just keeps repeatedly rebooting without ever loading windows.
I don't know if the system saw it as a RAID array or something, since both disks were adversely affected.
Unless you want to solve 2 problems at once, I'm content to just work on the first drive, as I want to clone it to save my data--while the "rebooter" had already been cloned earlier in the week--and can wait.
HDD#1 can boot into regular mode, but nothing works--not right-clicking or left-clicking on anything , not even the start button.
In safe mode, I'm able to use programs, shut down safely, etc.
I tried a "clean boot", which is to block all items in startup and disable all the non-Microsoft services from loading as well, but it did not solve the problem.
What else can I do?
I do not have original Vista disks, thanks to the computer maker being too stingy to include them.
I DO have a 3rd working computer of the same exact model, same Vista Home Premium 64 Bit OS with SP2, but with different programs installed, so maybe something from Vista can be copied from HDD #3 to correct problems in HDD#1.
Thanks for reading this far and for any advice you can offer.

Sounds like the mouse driver that you have installed is bad, as Safe Mode uses the standard Windows Vista Drivers. So in safe mode, go to device manager (start, type "device manager" then click on device manager). Next go to your mouse, and right click it, press uninstall. Reboot. Windows should install the necessary drivers.

Also, you could download the Nerosmart recovery disks from here, which should be able to help you repair the second drive (if it is able to be repaired.) One thing that you can try is startup repair.