Kryxal

This sounds like a job for ... WHACKJOB!

I'd actually transfer out of the return ship to a point, but that can be unsafe in a way.

If you're going to quicksave a lot on the way down, make a different save while still in orbit in case you do something unrecoverable then save again.

Oh, and define large ... tonnage should do.

I like the plane-matching one too ... specifically where you eject on the same side as Moho's apoapsis. Arriving at the periapsis and plane intersection is the most fuel-efficient transfer you can manage, just use your first burn to set up a later encounter.

Likewise, Z turns the engines on at 100%, though that functionality wasn't always there.

It's tough to measure those angles, most people go with the practical "ejection burn that is directly Duna-retrograde at SoI". Once you have about the right delta-v and exit direction, you can fine-tune with PreciseNode and knowing the changes you want: Increase delta-v to lower PE / decrease to raise Adjust burn position in the orbit to change ejection angle - going outward from the star gives Kerbin more time to catch up, inward gives less. You can also change by full orbits, but that could mess with your ejection from Ike, and if you add enough orbits (a day or so worth) you'll probably want to fine-tune your Duna ejection angle With these you can fine-tune everything but plane-change. For that, you'll want to set a node about 90 degrees before arrival, make your plane-change there and fine-tune your altitude.

Does it have a "have experiment on board" checkbox? If so, just try different ones and go to launchpad / revert (or recover).

Bombs would be aligned the other way around, but those you don't want to close again. In-game it doesn't matter, but in real life if you want them to close again you have them like in the picture.

Also, those widely-spaced engines mean you can trim your craft by adjusting the individual engine outputs.

Two problems with this ... unless it's close to aligned, you're probably outside the ability of the engine to gimbal far enough, and if you try to leave the trim set, will reaction wheels make you turn while not under thrust?

That ejection burn is more efficient than you think ... by the time you reach the ejection point, the Mun will be further along in its orbit. If you drag the node along the orbit and the AP and PE go down, you're improving the efficiency. Also of note, you only have to mine 2200 from the Mun, nowhere does it say the mining craft has to be able to store it all. Still, I usually build with ISRU and do a refuel on landing ... means you have LOTS of delta-v to work with!

Try to make your Laythe rendezvous at your periapsis, and heading in the same direction around Jool. If you're already in the Jool system, fine-tune your Laythe pass to capture via gravity assist, preferably with a high apoapsis, and fine-tune the next encounter from there.

You have just enough delta-v in that if you do it all right, but honestly that looks oversized and over-engined. For instance, switching stage 2's Poodle for a Terrier (and smoothing the 2.5m to 1.25m transition) will save you 4 tons and you don't need all that thrust. In fact, that one change will almost double that stage's delta-v. Your initial stage looks to SSTO-capable, and also has too much thrust. At the very least, switch some of the Mainsails for Skippers.

The biggest things needed to turn faster are more bank angle, pitching up some to maintain altitude, and not too much speed.

Kerbin's orbital period is 426 (6-hour) days. What you need is the time between identical alignments: (x / 184) - (x / 426) = 1 x = (426*184) / (426-184) = 324 (approx.) 1/4 of that is 81 days.

That sounds as recursive as Unix usually is...

I wonder if body lift isn't having a pretty major impact ... it's the only thing I could see making enough of a difference to cause flipping.

If Duna is at the 6 o'clock position with the view centered on the sun, Kerbin should be at the 8:30 position for a minimum-energy transfer, about your current situation I think. Launch to leave Duna's SoI directly retrograde. If it shows you arriving too soon, angle your departure to be a bit away from the sun, and you'll need to add a bit of delta-v to get the periapsis back down.

Ok, so you want to use a Clamp-o-tron docking port to attach the antenna later, so it's not sticking out on launch? Probably the easiest fix is to put a part between the two bays there, and attach the clamp-o-tron to THAT. Send the antenna up later. For that matter, that's a relay antenna, and I doubt you need that. Consider using 1-2 https://wiki.kerbalspaceprogram.com/wiki/Communotron_88-88

Parachute missions are simple enough, just use a suborbital rocket and place your apoapsis within the upper edge of the altitude band (for that one). Go straight up, return navball to surface mode if it switches. The research above missions can be done by plane or rocket, your choice ... so can the research below missions, but a rocket's going to end up landing. No idea about the building rollbacks, but why would you? Try destroying and rebuilding it, maybe?

It might be worth getting out and pushing at AP.

AP is in gray, you need to upgrade buildings. Once both tracking station and mission control are upgraded, you'll get nodes back and the markers and track will turn various colours.

The usual goal is to be somewhere about 45 degrees to the horizon when passing 10 km, or maybe a bit higher. That sort of depends on your TWR, though ... I can't judge your actual TWR and angle from what you said above, but I'd never succeed with the profile you seem to describe.

Be VERY careful, this sounds like the start of a loop that will make your plane explode (in size, though literal explosions aren't uncommon in KSP design phase). You think you need more of something, so you add it, then you need more of something else, and so on, and so on...