Well I can tune the samples per second a little bit. The most I can slow the digital signal 'cycle' is to about three seconds with 2096 analog measurements. So I quickly tabulated ~700 signals a second.
Unfortunately the triggering will not be absolutely uniform. I could try to design it for uniformity. There will be some hysterisis between the digital signals as they are coming from a motor encoder. So I can't exactly say the change in time from the first signal and the second(accelerating) will be the same as the 700-701(roughly no acceleration) or 2095-2096(decelerating). I haven't calculated how much deviation from the signal rise and fall-times or race conditions and do not unfortunately own an oscilliscope. I could try to come up with a rough estimate or attempt to tune a PID control on the motor/encoder to keep it with-in a certain range. However, with the interrupts going it's hard to say how much deviation from said PID control there would be if it was in say a main-loop.
That was why I was thinking that using an interrupt on the digital pin was a good solution, but if I had to use the timers on the ADC this would create a problem. Unless I settle on a time for the digital pulses and can have them delivered uniformly. I could get to work on this today if there is a good work around going this way. I was hoping to avoid going this route but can try if there is no foreseable other means.