Macenzie

I'm here to fly rockets and make explosions not count! D:

The only way I have managed it is to put the craft into a near geo-stat orbit and warp until KSC is about to be directly under me, then burn the apoapsis to geo-stat (and finally circularise). Like K^2 says there isn't really an exact science to this~

Pot Noodles~

Not had any issues here~

Yeah, sounds like you have the docking ports on backwards to me :S

Try the Kerbal Attachment System mod, you can transfer fuel with the winch if done correctly

I can confirm there is an issue with sheilded docking ports. I've also encountered the problem when docking a part using a tug to a station and not being able to use the "undock" command (the game ignores the button being clicked). This even happened to me last night when docking a part that had it's own command pod (so that isn't the issue). The only way to fix it is undock the part again, then undock the tug from the part, then re-dock with the part and finally re-dock with the station and you should be able to get yourself free. This has only ever happened to me when a shielded docking port is involved.