Just a short post here.
I have discovered the source of at least one of my problems. One of the leads on my thermistor is broken. I think it may have burned through when I had the thermistor and the heater wired backwards. In any rate, the thermistor reads as an open circuit and is definitely dead. I will have to remove the extruder and dismantle the hot end to replace it.
I have also made up a ground wire to run between the main and extruder boards. hopefully that will help to clean up the signals between the two boards and get the instructions to the extruder cleanly.