powertop is an open source project, even though it seems to cover all bases you can still attempt to contribute updated to add functionality, stability or make it more user friendly. You can visit their homepage to download the source from the repo, join the mailing list and begin working with their community to make the tool better.
One area where I think powertop is lacking is with being user friendly, how about starting by working on a graphical user interface to get used to the code then implement additional functions to improve the tool.
If you are content on starting a new similar project there is nothing to stop you, but since powertop is basically standard in most distros, adding features to that product will benefit large quantities of users much faster than waiting have a new project discovered.
If you are looking to add a custom kernel to a linux based distro installed in a VM then you would treat it just like a physical installation where you download the source, then compile and install it locally. If you are looking to build a custom installation without a distro then you will need a live CD image to boot into first, once the live image is booted you can partition, compile and install a new kernel as the base.
There are some live cd options ( http://lifehacker.com/5984707/five-best-system-rescue-discs ) that include basic malware and virus scanners, but most of the deep problems in windows are based in the registry which can be hard to read outside of windows. So, for you needs the best bet is launch a live CD with the AV/malware tools for a quick scan, then upon completion boot windows in safe mode to attempt ti find and correct problem in the registry using a tool like what is listed at http://pcsupport.about.com/od/toolsofthetrade/tp/free-registry-cleaner-programs.htm
You can install a linux based distro as a dual boot option along side of windows if you have disk space available or you can buy a small cheap embedded system like the raspberry pi and install a linux based distro on it. Using a raspberry pi you can setup a webserver, program new applications or even interface it with other devices for robotics.
I have already forwarded this message to a lead at the Linux Foundation, if they or their partners are interested in the idea then something may come from it.
Thank you for sharing the information here.