Here is my boat. It maxes out at a top speed of 236 m/s, I call it the "H.s Dragon" http://puu.sh/2G7IV/7ac24ca806.jpg http://puu.sh/2G7Gc/64e564b4da.jpg
You would need to counteract the force comming from the engines that are using their exaust to push it. Soo try put the same amount of rockets on both ends to stop it from deorbiting Edit. Sorry i didn't read your entire thing. It might work but im not sure if kerbal has wind effects :/
Yea its hard to dock at a low orbit because both the craft move a lot more when your not controling it. I find that the easiest docking is anywhere above 200km