To be honest your problem regarding the Alfa AWUS036H card seems to me a little odd. I'm using BT 5 since R1 and despite the one particular aspect about some specific Atheros driver the Alfa went smoothly anytime.
I'm not sure if in this point there's something easy that can be done to restore your system in a right order.
However, If I will be you I'll try to do the following:
1. REINSTALL the BT r3. I really didn't got the point why you've compiled some drivers for Alfa as long the BTr3 contains exactly what you need.
2. Try to connect using both wifi cards, one by at the time, to a wifi AP. Firstly try the most easy scenarios, no encryption. If both will work then upgrade the AP encryption to WEP and try again. And so on...I think you got the point, actually.
If at some moment something goes wrong then at least you'll know exactly the hot point and eventually some logs as /var/log/messages and maybe others can be checked up for additional details.
The easy step by step diagnostic will give more hints and knowledge than compiling drivers blindingly.