[Taera]

you might want to try using short-range weapons on your ATT. (dont forget the shields and armor... a lot of). Massive-mounted planetary napalm might do the trick (hehe - 1800 damage per 40kT per 2 turns)
......
guess what, if armed the ship will proceed to capture the target planet immidiately. Be careful though as in max tech three APB-armed M.W.P's can cream the transport before it comes into range.

And if im not mistaken, if you capture the WP's intact, you get them to work for YOU.