I know that when I installed HTC Home, it gave me the option to remove the clock from the top just because HTC Home has a great clock in it. I think I used KaiserTweak, look on
xda-developers - Powered by vBulletin for it. It is a great program anyways.
I'm not entirely sure about the bottom lauch bar but I think individual programs have to support it but I could be wrong.
If you are wanting the program that lets you toggle wifi, bluetooth, and various other connections, it is called Comm Manager in the dropdown from within Settings > Buttons.
I don't think that you can reassign the ok button on the side, I do know that you can get a cab file off of xda that can reassign the PTT button if you don't use it. Hopefully those answer your questions