strongest_2hu

It looks like the port is attached to an adapter, actually, which is then attached to the yellow 6-way structural connector. I think the problem might be the adapter, I've had trouble with them being really wobbly and clipping right through other parts under load in the past. It looks like in the second picture that the two ports are doing just fine but the adapter is dug about 5 degrees into the docking port. I think you should try something similar minus the adapter.

KSP lighting in a nutshell.

You don't want the rest of the craft to use the fuel in those tanks until a time of your choosing, right? Use docking ports to attach that tank array to the body of the craft, then right-click -> "disable crossfeed" on the docking port. Enable crossfeed when you've detached the rover.

I think unless you dock extremely inefficiently you will either grow tired of the mission or lose it to an update before you run out of RCS fuel, and if you've got a kethane extractor you'll never run out. It doesn't take much to dock something like that to something similar, probably no more than 5 units of monopropellant or so, as long as you use the main engines to provide forward thrust (just shut a bunch of them down if there's too much thrust) and are able control the ship you're docking to: just switch back and forth between vessels to keep the docking ports pointed directly at each other (using command-module torque) while you drive it in with the mains. If you're going to add RCS blocks for routine attitude adjustment, never forget that lander-can has the same form as a big RCS tank but weighs less and never runs out of torque. Command module torque is god's gift to kerbal-kind, use it early and often.

Easy mode: remove three of those four huge RCS tanks. 10 tons gone. How could you ever hope to use that much RCS fuel in normal orbital docking operations? Harder mode: are those the stock tailcone things holding those engines on, and if so, remove them because that is 2.4 tons of dead weight. Hold the engines on with cubic octagonal struts or something. Beyond that the only way to get more power is to use more engines or more powerful (less efficient) ones, either of which will reduce your delta-V. The only way to get more delta-V is to carry more fuel, use more efficient engines, or reduce non-fuel weight. These are decisions that only you can make based on what you need or want.

Because scanning as-is is neither fun nor difficult, merely time-consuming. "Half the work" you mention has been described by KhaosCorp as "leaving the game running for 20-30 minutes while you go do other stuff." Loads of fun right there. Might as well ask why I use time-warp when I send off interplanetary voyages.

I'm trying to use the debug part on my scanning satellites so I don't have to waste 10-40 minutes of my life watching dots get drawn on a rectangle. I was hoping it would have an export to map function but sadly it does not, nor does it have mouse-over coordinates, making it difficult to relate the position of a deposit to that of other spacecraft. I think the best way to get around this is probably to drop a small lander with the debug part right on top of a deposit as a beacon to guide in your miners and converters. It's not quite as nice as having a filled-in scanner map but it can fill the gap until we either get swath scanners or the current scanners stop losing data points at high time warps.

As part of my experiments in aerial refueling with KAS I put two airplanes up at the same time, it was actually really simple and the only stipulation is that they have to stay within the 2.25km of each other (you can of course increase that with mods). Basically you launch one plane, drive/fly it off the side of the runway, then switch back to space center to launch another plane. Now you have two planes sitting near each other. Throttle one up, pitch up and engage ASAS (throttle back if exceeding 2.25 km is a factor), then quickly switch to the other plane with "[" or "]". I know it doesn't make sense, but I've never had trouble switching between throttled up planes in the atmosphere. From there you quickly throttle up and race to catch up with the other plane. As long as you're within 2.25 km you can do whatever you want. Sadly my aviation pioneers were unable to refuel one plane from another, as the refueling boom proved unstable and impossible to intercept at speeds slow enough to allow docking and preclude explosions.

Why are there three kerbals stowed away on the big telescope, invisible until it crashes and they show up dead in the launch report? Edit: I added "crewcapacity = 0" (or whatever it is that the probe cores have) to the telescope and now there are no kerbal passengers.

It's clear that you have a good grasp of multiport docking from your screenshots in the original post which everyone seems to be ignoring. The problem you've caught up with is that docking with multiple ports out of plane with each other is extremely difficult. It seems like no matter how well you nudge them into place one plane will get the magnetism effect first and prevent the docking of the other plane. However, it can be done: I have a nearly identical setup (2 sets of 4 port symmetry around 4 objects docked up in a square) in orbit right now with all 8 connections showing as docked, which I did by bringing the last piece in extremely slowly and at an angle such that both sets of ports got the magnetism at pretty much exactly the same time. I won't recommend it though, as even though it shows as docked one of the ports is visibly misaligned and separated. I suspect this is the cause of the phantom forces that are slowly making the entire structure rotate faster and faster over time :-). Your best bet if you really want to go through with construction as planned is to remove the out-of-plane docking problem entirely. In your OP screenshot, I would suggest undocking one of the two existing pieces from the station, docking it with the new piece, then docking the whole assembly back with the station. That will put the four ports in question in the same plane and let you easily dock them with normal multiport precautions. It makes the whole thing pretty tedious, but I don't think there's any other way to avoid the problems you're having.

New in .20. Not sure what use it is unless you put your command module on backward.

F4 toggles ship labels. You don't really need them for docking, though, typically I fly off the navball until I'm at about 300m and by then it's in visual range (possibly because I accidentally turned off the ship labels when I first started playing and didn't figure out how to turn them back on for a long time (I think it happens to everybody at some point)).