passive high pass filter to iphone mic jack
You correctly reduced the impedance seen from the iPhone from 100k to 1k, and you kept the RC constant the same by increasing capacitance by a factor of 100.

However, you are now requiring 100 times as much current to flow across the resistor to get the same levels you saw before. It is unlikely that the unspecified source can drive that much current from the pulse measurement

Recall that sources need to be much lower impedance than their loads to drive them without significant distortion of the original signal. Typically bioengineering sources (like the pulse) are very high impedance, because the body simply does not produce that much energy.

The solution for driving a low impedance load from a high impedance source is to use an operational amplifier. These have very high input impedances (so avoid affecting sensitive circuits) but have very low output impedances (so can drive low impedance loads). 

I think restoring the original RC combo, and then adding a voltage following opamp driving the iPhone 1K load will solve your problem.