Converting Pulses to Analog Input for Mic
Given the unknown limitations of the mic inputs of various devices you have to design conservatively.  

If you are always going to be sending just the pulses from two flow meters you can use pertty specialised modulation techniques. 

Knowing that you will need to decode the signal in the device you want to maintain a relatively simple modulation scheme. 

Given that the bandwidth should be low you have some flexibility.

I suggest you use amplitude modulation and frequency shift keying (FM and AM together)  at these low bandwidths you will likely be able to have simple modulation systems.  I would specify a 8 pin microcontroller for the modulator.

If you have flow sensor one wired up to generate 1300Hz and 2100Hz for the two states and flow sensor two wired up to modify the amplitude between 30% and 70% of maximum you should be able to send the data over almost any kind of audio signal path.

https://en.wikipedia.org/wiki/ITU_V.23

If you do not want to rely on amplitude modulation you could use a dual tone system like a DTMF phone and use the two flow sensors for the row and column selects on the top and bottom rows and the left and right columns. This will require a bit more smarts in decoding but even a PIC micro can do it so a smart phone should be fine with the job. The tones for the one sensor would be 1209 and 1633 HZ and the other would have 697 and 941 Hz, these are not harmonically related and well within the audio band and can be separated from each other easily. Generating these signals in a micro is possible but a bit harder though there are examples out there.  There used to be ICs that would do this for you from digital inputs requiring a few passives and a crystal.

https://en.wikipedia.org/wiki/Dual-tone_multi-frequency_signaling

Just to add to your results so far.  All the mic inputs will be different.  The DC coupling capacitors will make low speed digital input a problem, converting your initial 4 level analogue system to AFSK with a 555 or similar is also a workable solution.