If I understand you correctly, you want to connect the Kindle to the computer in some way and, while reading the Kindle, use the PC keyboard to turn the pages and make notes and annotations on the Kindle. As far as I know, there really isn't any way to do that - in fact the Kindle is designed to be able to use all it's features even if you don't have a computer at all. You could use Kindle for PC instead of the device itself and then sync your notes etc so that they're available on the Kindle.
The only thing you can automate on the device itself is the page turning - by using a work around with the Text To Speech feature. When using that, the pages turn automatically in time with what's being read out - if you turn the volume down, you can just read without having to use the page turn buttons - useful if you're doing something else, such as using a treadmill. The down side to it is that you have to read at the exact same pace as the TTS is running.
I can't think of anything else that would come close to what you're trying to achieve. Anyone?
And I almost forgot!
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