I think you are asking in the wrong forum. You sound like you just want to know how to use this LED sign controller you just bought, and are not interested (at all) in reprogramming the Altera FPGA on the (custom?) controller. This forum is for FPGA related issues.
I would suggest that you look for some kind of vendor ID or part number on your controller board and try googling for for that and see what comes up. It may very well be what you have is a custom design and unless you can find the original designer you may be up a creek.
The panels themselves look to be of a pretty common design (google 32x32 led array) and I even have one of them that I connect thru the 10p connector to an Arduino. Your assembly looks like a larger array of these 32x32 sub panels.
