It'll fit easily, you just have rotate the shroud 90 degrees. Use two fans, it made a 5C difference for me. The fan on the shroud MUST suck. The other fan should be rotated 45 degrees and blow, sucking air from the DIMMs direction. I used nylon ties to attach it.
Also, the PEP66 doesn't like overpressure, it'll make the temps go skyhigh. I tried that and my temps went so high that the machine rebooted. Checked the temps after that in the bios and they were 66C.
I have the same Alpha and mobo. There are a couple options. One, rotate the shroud so that the fan sits on top and pushes air down accross the fins. You may need to drill a couple holes in the fins, but if you do it just right, the screws will fit between the fins and hold the shroud in place.
Second option is getting a couple slimline fans and mounting them on the sides. There is a teeeeeeny bit of room left over. Have one suck and the other blow. Try looking at www.coolerguys.com/ and peep the setup they sell there. They have one specifically for your Abit KT7A mobo.