I don't know much about wireless routers, but maybe I can help get your started.
If you're going to compare antenna A to antenna B in some way, you need a way to measure signal strength on the receiving end and you wouldn't want the signal meter to be pegged at max for both antennas, because then you don't know anything. So you need to make the signal sub-max in some way, either varying the transmit power, varying the receiver gain, or increase the distance between the two.
It looks like the routers use SMA connectors, so you can make your own jumpers to connect to your antennas. Just poking around with Google, I found this auction in eBay which might give you some ideas on how to run your experiment:
http://cgi.ebay.com/3in1-12dBi-WiFi-...46339513QQrdZ1
Maybe that will give you some ideas of your own.