Hi!
I would use a common PC in some small form-factor, (not a PC-104 board, wich have, in general, expensive hw) with NI DAQ boards:
-cost of PC: ~2000 $ (a rugged one, maybe fanless is better....), with a solid state disk (Hitachi is a major producer...).
- 2 X NI 6509, 96 DIO each, 249 €x2 (quite cheaper and reliable, if you don't need synchronized IO)
- Multifunction DAQ board(s), I don't know exactly what do you need.... as sample rate, (for Low cost, PCI 6010, 329 €, and for Analog Out, PCI-6722)
The major cost can be PC and analog out board.... Of course, you can develop a uC based system, but time-to-market will increase (and you have to be carefull in signal conditioning...).
For embedded PCs, I know two manufacturers:
digital logic (vert good boards & very reliabile), and
IEI (quite good..lower price..

). Also
Kontron is a good manufacturer, but I evaluated too few products to say more....
You can find also (if my memory doesn't fail...) some PC/104 IO boards from Digital logic, but check with your budget....
Hope this can help! Have a nice day!
graziano