Problem fixed. The re-root tool is now called "assembly anchor". I could not have come up with a worse name if I tried. It is pretty obtuse just like last time. Even after choosing the new "anchor" you have to fiddle with the movement tools at the bottom to get to the point you can actually move the thing. Be sure to save after choosing the new "anchor" and before you merge the pieces together as this can still sometimes trigger the random trusses direction bug.
edit:
I spoke too soon. Loading into the runway or reloading the saved merged file results in terrible bugs. The docked vehicle falls apart on the runway and disappears completely when reloaded in the VAB. I finally see the extreme bugginess people are talking about. I am so slow with the game that I am only now discovering the bugs. I spent too much time fixing performance problems and building that I did not realize how broken the game is.
edit 2:
The docked vehicle falling apart bug and/or becoming missing in the VAB was due to attaching to a part that was attached to another part that was attached to another part and so on... I changed the root part of the vehicle and was able to attach implements directly to the root part. The root part can be most anything but crucially it does not have all the "baggage" that parts attached to other parts have.
Unfortunately I am still finding the process nearly impossible. See these bugs:
I suppose I will redesign the ground vehicle from the "ground up".
