Rover31,
I am pretty sure that will fix your issue. It appears looking at the gt2560 board that the step and direction signals come directly from the MEGA cpu chip. Many designs these type signals are buffer through another chip but I do not see anything in the photos, so that is most likely your issue. Reversing the driver board probably sent the driver voltage back into the MEGA chip with burned those output transistors on those ports.
I know this is an old thread, but I believe that board won't allow the extruder motor to run if the hot end is below a certain temperature. Just a thought for anyone else who might be here looking for an answer. Make sure the hot end temp is at least 170 C before testing.
Thanks for bringing this back up I should have come and updated it!
I could not figure out the problem but a great guy in the Seattle area did find and fix it.
My original board had a blown fuse (why oh why did I not check that!?) and the steppers drivers that I purchased did not have the correct voltage rating so luckily I had an extra of the original ones. So on it went and the unit runs as it should now.
So check your board out thoroughly before spending/buying a new one. My original board is totally fine!
Thanks to all suggestions!!!