Help with low-pass filter and TTL logic interface
So I solved the problem.  I built an opto-isolator using an IRED and phototransistor and some black tubing.  This effectively eliminates the EMI and gives me a clean square wave.  Note that some applications may require a resistor on the base of Q1, but in this application the resistor is already present on the control board as shown in the previous schematic.

For the phototransistor I used some left-over GE L14GX536 parts in my bin.

Here's a schematic of the final product, in case it's helpful to someone: