It sounds to me as though you have an intermittent open (This is where somthing that is supposed to be connected is not) On the other side of the coin, a "short" is when something that is not supposed to be connected or touching is. Without me being there with a VOM meter to test the power side of each component, it is impossible for me to tell you exactly where the issue lies.
There are several components that could be failing however the fact that light blinks leads me to believe that it is probably the logic board.
Some components that fail that could cause the door to stop due to an intermittent open in the circuit are as follows:
The safety Circuit: However the LEDs are staying on...
The Logic Board: Logic board PART NUMBER: 41A5021-3H-315
The Limit Switch: Limit switch PART NUMBER: 41D3452
The RPM Sensor: You said you replaced this already.
Many certified technicians stock these parts on their trucks so that they can just start swapping parts until they locate the problem. We unfortunately, do not have that luxury.
Some techs actually know how to use a VOM meter however, many do not.
You can try replacing the limit switch first as it is only $25 compared to the logic board at $126 however, if it is not the limit switch, then I have suggested the wrong option. You might consider calling a service tech as this issue really demands a hands on diagnosis...