Zelnogrard

That's true, my bad. The reason I circularized was because I intended to setup an encounter with the Mun for a gravity assist out of Kerbin SOI, and didn't want to bother with synching orbital periods or whatnot. Not even sure if free d/vs from assist cover the circularizing burn, though they probably should. So my previous post might have been misleading, TC should just go with the "Pe kicks" method.

After a bit of practice, EVA controls aren't that hard. And instead of waiting for devs to implement this feature, you can use the Crew Manifest mod to do the transfer.

Now that's a weird problem. If strutting helped with it, then it sounds like it was some structural failure in a long stack of modules. Sometimes the modules get detached without being disintegrated and just stay on top of each other. But then again, if the same thing happens with the ship fixed on the launchpad, the said type of failure is out of the question. Anyway, I'm glad you found a solution. p.s. yeah, premoderation It's ten posts only though.

Looks like you're running out of electric charge, unmanned control unit need it to respond to controls, otherwise they just freeze. First several times I got that I thought it was some glitch. Hitchiker cans come empty by default, so no help from kerbals. Putting one (or more, but one unit should be enough) "PB-NUK Radioisotope Thermoelectric Generator" on the payload stage should solve the issue.

Seems like a bug to me. Perhaps, some parts of the lander clip with each other? Or the undocking itself causes the removal of some struts and (possibly, only guessing here) some collision-redetection subroutine to kick in, causing disaster. Another thing to try: try undocking via the larger port, and after that undocking the secondary command pod. If it goes well, you could just reassemble the thing and continue from there.

One thing that helped me to make these long burns more precisely was performing them in several steps whenever possible. For example, when going from LKO to the Mun, you rise your apoapsis and circularize repeatedly until you need only a moderate burn to get the Mun encounter. That might not be an option when timing is crucial, though.

First thing that came to my mind was to try the same operation under slightly different conditions. Turn the SAS/ASAS on or off, fire up some of the lander engines, apply some spin to the entire ship before undocking (that's probably the silliest one). My first Duna-capable ship with a lander had a nasty habit of disintegrating randomly after switching to it via square brackets, but quicksaving before trying to switch saved me.