1. There are many configuration tools included with the different distrubutions of GNU / Linux ... what you are trying to accomplish will determine which distro you would pick.
2. The PCI bus is the interface between PC cards (like a network card, video card, sound card) and the computers processor ... devices built on to the motherboard (one's that are not external cards) also go through the PCI bus. There is really only one speed, and it is 33mhz for modern PCs. (
here is a link)
3. You would need to either pick an SMP kernel, or recompile the kernel with the memory selection set to 64GB (that is for all systems where the physical RAM is more than 4 GB). The kernel option that needs to be set (in the kernel config file) is
CONFIG_HIGHMEM64G=y.
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What do you want to use this computer for?