If you decide to stick with analog communication, make your transmission differential. Analog diffrenetial OUT may seem a bit exotic, but google for it. If your analog is TRULY differential (not just SC ground and signal) you get a tremendous improvement in noise rejection.

Totally right!

Maybe it got lost, but have a look a V/F converters.

If I remember correctly, Raghunathan told, that signal bandwidth is up to 1500Hz. It's not easy to design a V/F converter, which can handle this input signal bandwidth, because lowest frequency after V/F conversion must be much higher than maximum frequency of input signal, otherwise an integration would take place resulting in unwanted low pass filtering of input signal.
Also, Raghunathan needs 12bit resolution. It's possible to have a LM331, RC4151/2 or SSM2031 running at frequencies higher than 10kHz, but then linearity suffers. At 100kHz nonlinearity error of RC4152 is -0.07% typical. So, he would loose two bits.
Not enough, V/F would have to work with an offset, so that an input signal of 0V would yield a frequency of let's say 10kHz (<1500Hz!!). At input signal of 5V output frequency could be 20kHz. This would improve linearity due to lower frequency, but offset fabricating additionally introduces some error. So, for me this seems to be a difficult task.

A true differential amplifier, on the other hand, is much easier to use. And it's no problem to achieve 12bit resolution.

Kai