We generally want to keep the configuration of the 40m close to that of the LIGO sites, which is why we chose BusWorks, and it is also being established as a standard in other labs on campus. Of course any suitable DAQ system can do the job, but to stay relevant we generally try to avoid patchwork solutions when possible. Did you follow Aidan's instructions to the book? I haven't set up a system myself, yet, so I cannot say how difficult this is. If it just won't work with the Raspberry Pi, you could still try using a traditional computer.
Alternatively, following Jamie's suggestions, I'm currently looking into using python for the modbus communications (there seem to be at least a few python packages that can do this), which would reportedly make the interfacing and integration a lot easier. I'll let you know when I make any progress on this.
About acquiring data: Initially I couldn't start with proper Acromag setup as the Raspberry pi had a faulty SD card slot. Then Gautam gave me a working pi on which I tried to install EPICS. I spent quite a time today but couldn't setup acromag over ethernet. But, it would be great if we have a USB DAQ card. I have found a good one here http://www.mccdaq.com/PDFs/specs/USB-200-Series-data.pdf It costs around 106$ including shipping (It comes with some free softwares for acquiring data) . Also, I know an another python based 12bit DAQ card (with an inbuilt constant current source) which is made by IUAC, Delhi and more information can be found here http://www.iuac.res.in/~elab/expeyes/Documents/eyesj-progman.pdf It costs around 60$ including shipping.
About temperature sensing: The RTD which I found on Omega's list is having a temperature resolution of 0.1 deg C. I have also asked them for the one with good resolution. Also according to their reply, they have not performed any noise characteristics study for those RTDs.