Frozen touchpad and keyboard on HP Pavillion dv6 3225dx Notebook

Extremely frustrated I've looked and tried to find a solution to no avail. When the notebook boots up, it gets to the login screen, I wouldn't be able to do anything at that point but I can log in because I have a fingerprint scanner, from there I'm 100% dead in the water. The only way to shut down is to hold down the power button. While the computer is in bootup, I have touchpad/keyboard function, I can escape to boot options, BIOS, repair, etc. and have normal functionality while there but not in safe mode. I have ran SFC with commands several times, chkdsk with commands several times, nothing changes. SFC says it found problems but was not able to fix all of them and the last chkdsk found nothing wrong.

Here are the events leading up to:
* had disk errors and bad sectors in old hard drive (could not repair)
* cloned old hard drive to new hard drive (there were errors but the new hard drive booted and worked for the most part correctly)
* in the process of trying to fix missing setup files for applications and other miscellaneous small issues, I ran troubleshooting, updates, chkdsk, sfc, etc. removed various applications, and added a few, nothing worked. I installed Revo uninstaller to remove Kaspersky Internet Security as it is THE MOST stubborn application to remove I've ever experienced. The reason I mention that is because I went through my computer trying to find the leftover files even after Revo because Kaspersky was still running after re-installing it and uninstalling it again. There were some files in System 32 that had kaspersky attached to it's description. I stopped them from running and deleted them. They were close to the kb files and after researching which files to remove I remember in the end of the post it said it wouldn't delete a certain file beacause you wouldn't have keyboard functionality. I made sure I didn't but I can't help to think now that out of the 6 files I deleted (some of them kernel) I may have deleted the mouse and keyboard files in error.
* I tried a System Restore of the most recent point prior to the issue and it did not work. I think now that I should have tried it again at an earlier point but didn't and I did that from the repair module obviously since I couldn't do it anywhere else. I have tried since to do another but the restore points have disappeared.
* The last time I had a working touchpad/keyboard in Windows, I ran sfc /scannow /offbootdir=d:\ /offwindir=d:\windows at boot in the command prompt. I got the same message that, it found errors but did not fix them all. Then I ran chkdsk /f /r from boot at the command prompt. When I returned to my computer after a couple hours, I rebooted and no longer had a touchpad or keyboard.
I am up in arms and extremely frustratd as I feel I have tried absolutely everything to get them to work again. I hope that the only option I have left is to format and clean install. I do not have a full back up and can't get one fully executed at this point.
Please help!!! Thanks in advance to any suggestion and assistance that you may be able to provide, it's much appreciated!

The following link is to the support page of my Notebook.

http://h10025.www1.hp.com/ewfrf/wc/product?product=5051461&lc=en&cc=us&dlc=en&lang=en&tmp_track_link...

Thanks for the reply Britton30. I DO have a wireless usb mouse/keyboard however, they only work as the touchpad/keyboard do, in recovery/repair mode. I don't think the wireless would make any difference. I have tried a repair install, however when I get to the upgrade click, the error message reads, "The computer started using the Windows installation disc. Remove the installation disc and restart your computer so that Windows starts normally. Then insert the installation disc and restart the upgrade. (Do not select "Custom (advanced)" to perform the upgrade. "Custom (advanced)" installs a new copy of Windows and deletes your programs and settings.)
I cannot login to Windows because I have no mouse/keyboard, hence I cannot perform the upgrade/repair install.
Will the, "Factory Reset and Minimized Image Recovery Options HP Pavilion dv6-3225dx Entertainment Notebook PC | HP® Support" wipe my original C Drive out? If so I am trying to avoid that. I don't understand why everything works except in the main Windows. I have even installed a Linux system via Ultimate Boot CD on the memory and I have full functionality there as well. Your assistance is greatly appreciated...