Want to build my first mill / extruder combo

Hi everyone!
My first post, new to this forum.
I'd like to build a versatile CNC mill and then add extruder capability like of RepRap.
The machine is to be used at home in my garage for some light prototyping. Target usage of about 2 times a week perhaps, not for mainstream manufacturing.

Basic requirements:
Precision of the machine is top priority. XYZ moving assembly and drives need to be tight.
Cutting / milling aluminum and brass is a good baseline for strength and power of the machine needed. Some light work with steel would be nice too, but not a must.
While able to work with harder materials such as metal, the machine needs to be able to do fine work such as prototype PCBs for SMD parts.
The moving assembly needs to be 3 axis (XYZ), with about 12 inches of travel in both horizontal directions and about 6 inches of vertical travel of the working head.
Controller board needs to be as versatile as possible. Needs to be supported by as much software as possible. While using this controller for milling, it needs to also be compatible with software for extruder.

My vision:
The strong XYZ assembly should be the base of the machine, and tools should be added on to that.
Overall design of the moving assembly I like, from the short experience I've had with a locksmith CNC, is having the table move on two axes, and the working head moving up and down. Moving the table / part move instead of the tool should enable the working head to be mounted as securely as possible. Also not having the move the weight of a heavy AC motor around should also be a plus.
Having done a good job with the moving assembly, why have a single purpose machine? Let's add extruder capability to the existing XYZ setup. Extruder head may be detachable, or perhaps even on the machine permanently, beside the milling head.
I'd like to use prefabricated parts for drives and moving parts for precision whenever possible. Things like rails and shafts can obviously be cut to length, I have an AC grinder and a Dremel for that. For drilling I have a brand new 2/3 hp drill press.

My background:
I am 23 years old, a Computer Science and Computer Engineering student at Virginia Commonwealth University.
I work as a researcher in the Computer Engineering department in field of clusterization / cloud computing, and virtualization.
I have also done contracting work developing specialized small-medium business applications, such as service managers for service shops.
I currently hold 6 industry certifications.
My programming experience spans the last 11 years, many languages and paradigms. I have also done MCU and FPGA programming.
I have studied drafting and architecture for 3 years, and during that time I picked up good experience with 3D CAD solutions such as SolidWorks, Autodesk Inventor, PTC Pro/DESKTOP. Some Autodesk AutoCAD experience as well.
My robotics experience includes building competition robots (130 lbs to give you an idea of scale), mechanical fabrication, control systems, programming.
I'm a car nut among other things, but this isn't the forum for that :)
I design and build hi-fi amplifiers as a hobby.
To sum it up, I'd say I'm up for the task.

What I need to know:
I don't know much about the CNC market, like who uses what software and what controllers, what CAD software is used, essentially what works with what. Is there a good place where I can get this background information?
Has anyone done anything similar?
What are the most successful designs?

Budget:
For now I have allocated $1500 to play around with this. For a grand I want at least a solid XYZ setup and some milling capability. Extruder can come later.

Well, I think that's enough for a start.
Help is much appreciated and I am very open to suggestions.

A mill with a 12x12 XY work envelope with the ability to do smooth cuts in aluminum and cut steel in a pinch. Unless you have access to machine tools that's going to be a real challenge at $1000. You could start with a X2 mill and start hacking as seen here:

Projects 6

Hoss is a regular in the Benchtop forum, maybe he'll spot this and chime in with some cost estimates. It's the Y dimension that's unusual for a small mill, 12" Y is found more commonly on mills weighing in at 1000lbs+.