It seems to me that the FIR part of the project is well in hand, with the Matlab design.
For stripping the high-frequencies, I would not bother with anything more than a single-pole filter. Just crank up the sample rate until you can be absolutely sure that the nyquist frequency is completely covered by the analog filter. Even though you are looking for very low frequencies, there's not much penalty for using a high sample frequency. Either just use a large FIR filter to directly find the frequencies of interest or use a digital filter (of any sort) to strip the frequencies above the final sample rate's nyquist frequency before decimating.
My favourite reference on DSP: The Scientist and Engineer's Guide to
Digital Signal Processing
By Steven W. Smith, Ph.D.
My favourite FIR filter design tool: TFilter