I've had very good experiences with PCBCart, excellent choice 
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Yes, i did so two:) they also have a very good and fast support.. The copper thickness can be selected: very good, we may need more than the 35µm default. The 8mil minimal via diameter is even better (though you get less current through a smaller via)! The 8mil line width and line spacing are a problem, though: I cannot get an 8mil wire between two pads of the FPGAs: the clearance is too small. This problem can be solved by using more vias and routing everything on the other layers, but is is less than ideal.
There are "special PCBs" on the pcbcart webpage, though: 4mil for both specs. And they offer much more copper! I wonder how much that costs?
The point I made about the clearance depends on which pad diameter you use. My library used 0.5mm pads, but I read somewhere that 0.4mm may be sufficient. Any insight?
I have contacted them already they would also give us a price quote if we send some gerber files of a nearly final design and a BOM so they would also do the assembley.There are "special PCBs" on the pcbcart webpage, though: 4mil for both specs. And they offer much more copper! I wonder how much that costs?
The point I made about the clearance depends on which pad diameter you use. My library used 0.5mm pads, but I read somewhere that 0.4mm may be sufficient. Any insight?
Currently i am modifying your layout and routing to fit a 4 layer PCB. Acording to my knowledge alls unused IO pins are bound to ground by default so i changed this in your schematic.(please someone verify this).
I added the MSP430 and will custom build the voltage regulators and add the power connectors.
Saddly i asume there is no way to merge the egale layout files automatic.(this used to be a lot easier with Altium.... I am totaly new to Eagle) And the library of eagle is confusing me over and over again.
We should define some fix dimensions and global rail namings to be abled to on this side by side.
Board : 133mmx60mmx1.25mm (DIMM standart with increase heigh)
4 layers
Vccint: 1.2V
Vccaux: 2.5V
Vccio:2.5V