I dunno if this will help you out or not, but I was able to use what cgkades posted successfully. Thanks cgkades!
A little background: I am using the alfa as I said (which is awesome btw) and I believe I am using different drivers from you but I also have wmaster0 ( which appears to do nothing ) and wlan0. So, the commands I am using are:
This changes the mac address for wlan0 and I am then able to connect to the network through network manager, I haven't tried it on the command line. Macchanger will not work. Also, I am assuming you're mac spoofing because your cracking WEP or what have you. Once I put the card in monitor mode "mon0" pops up with the original mac address again. Macchanger works with "mon0" but if I do "airmon-ng stop" then "mon0" gets destroyed, so instead I have to do:
ifconfig wlan0 down hw ether <mac address> // without < >
ifconfig wlan0 up
And then I have mon0 in monitor mode with spoofed mac as well as wlan0 in managed mode with spoofed mac..and of course when I want to connect to the AP I use wlan0.
ifconfig mon0 down
macchanger -m 00:11:22:33:44:55 mon0
ifconfig mon0 up
I am doubting this will help you much since others already posted essentially the same thing but I wanted to post back that I at least solved my problem and maybe it will help someone else out. Good luck.