Help with custom build specs

I am about to begin building a PC which will be used as the brains for a CD Ripping robot. The robot itself is controlled via serial (RS232) interface and is used to move discs from spindle type stacks of discs to one of the drives in a stack of optical drives.

As a software engineer, I will have no problem creating the apps to do the required work but I am not really up on the hardware side of things. What I am looking for is advice on the components best suited for the build. Here are some factors which I believe will have a bearing on what my best choices might be.

1) I have a few different versions of these robots. The only difference is the number of optical drives. The smallest robot only has a single drive while the biggest has six.
2) The optical drives I will use (based on their DAE features and performance) will be IDE Plextors. Although I suspect they will be interfaced to the host PC via an adaptor and eSata.
3) Within the robot case, space will be limited such that a micro ATX board is probably the biggest board I can use.
4) The ripping software will be multithreaded allowing the system to be ripping from all drives simultaneously.
5) Additionaly the encoding (from PCM to flac) will also be done as part of the ripping process and will also be multi-threaded.
6) The Plextor drives I plan to use are rated at between 40X and 52X (three different models) read speed.
7) Encoding will be done mostly in RAM so the mother board has to be able to support large amounts (4GB maybe more) of RAM.
8) To support the large amounts of RAM the PC will be running a 64bit version of Windows (most likely WinXP pro x64).

I expect that data throughput will be the bottleneck while ripping and processor/memory speed will be the bottleneck for encoding.

Given these requirements can some of you hardware gurus out there suggest some options. What I would like to see is a disscussion on the pros and cons of various components so that I can follow along and hopefully learn a thing or two.

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  1. I thought I would add a few more bits of info.

    Speed of the ripping process is THE main concern. As such (due to the multiple threading of the encoding) the mother board needs to support a hyperthreaded multi-core CPU (ie. Intel Core i7) and fast RAM.

    No fancy audio or video is required, simple inexpensive on-board solutions would probably be best. Also the PSU is of no real concern, I will use whatever is required.
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