I am very interested in your Bricktronics Megashield. In looking over your schematic (v1.01), it appears that for each motor only one TACH line is connected to an interrupt line. This cuts in half the accuracy we could achieve by getting an interrupt on each TACH line.
In a future revision of the board, would you consider routing the two TACH lines for each motor to an XOR gate and then the output of the XOR gate to the interrupt line. As long as TACH2 status is still available as a digital input then direction could still be determined on each interrupt based on the current state and one previous state of the TACH2 line.