Aeroboi

While struts add drag It seems the cross angle matters so placing it as much vertical and as short as possible should help (which is best anyway)
I also heard but I am not sure that the parent attachment part of the strut connector influences the drag. If that part is a nosecone or a wing piece then drag would have been less.
I think this is proper, lage cillindrical tubes create drag vortexes and increase as you fly faster. For that matter, using no struts and attaching mk3 fuel tanks together and they'll hang as if they were loose. Using autostruts when necessary it's like bolting the fuel tanks on, and only the strut connector is used when necessary.
Also, the shock cone intake seems to do best for minimizing drag at super/hypersonic speed. Use it coupled with the 2.5 to 1.25m adapter and you will have the most aerodynamic shape. If you have Making history for 1.875m the FL-C1000 fuel tank seems to be the best shape.
Furthermore, what people always forget to mention is the amounts of stacks used. If you have a 1.25m fuselage but you require 2 engines it's better to use a adapter on the back then to create a second fuel tank.
If you have a space plane with 3 fuel tanks (1 center and 2 parallel) and you require more then 3 engines you'll also use adapters.
Also, drag also depends on the rear tapered ends. If it's only engines on the rear attachment nodes it is influenced by the engines, some give more drag. When using the R.A.P.I.E.R.S. you can use the reversed nosecone trick to minimize drag further.
Furthermore, while wing incidence helps you want to calibrate it so that the prograde reticle is at the horizon when you are at the crucial 400m/s mark. While some just take a simple ballpark of 3 degrees while 4 or 5 might be better. That means you'll break past 400m/s easier and also use less fuel.

Besides craft aesthetics my experiments (based on heat tolerance values and use) The most heat resistant part is a inflatable heatshield, also a deflated heatshield. If your stack is 1.25 , 1.875m or 2.5m it can rest behind the deflated heatshield. It isn't as aerodynamic as a fairing but not bad and should help your incentive to aerobrake. While it looks ugly I once managed to clip a fairing under the heatshield by dragging the heatshield out, build the fairing within tight margins and then lower to see if it's build right and then repeat. There's a slight threshold at which the point of the fairing goes to far to the top where it will suffer heating damage. That's probably directly under the node when the heatshield is inflated.
Another method I found is that you can place empty 2.5m ablator heatshield within a 2.5m stack to redirect the bow shock if heat cripples away with the checkerboard shrouds.
Besides that the best use are the ablator heatshields and ultimately the fairings. If using a winged craft to aerobrake enough wings and good attitude hold of 90 degrees should be good enough on 2400K parts if aerobraking and a fairing is capable of 2700K. The biggest issue is earo capture which involves interplanetary encounter speeds and is done with heatshields often. Fairings being able to withstand more heat should work better but have a lot of drag that goes with it so you need a wing or rear fairing design or anything else that drags to counteract otherwise your craft will tumble I expect.

The point in gravity assist's is not that it speeds your vessel up but changes it's trajectory relative to the greater local gravity well. Usually That is the sun, in the Joolian system it is Jool. So what you want to do is enter the target planet (on which you want to use a gravity assist "Tylo" apparently.) on the right or left side depending on whether it is left or right from jool relative to the *ecliptic (*relative to which is left and right)
So if you want to decelerate using Tylo play with the maneuver node by dragging the radial/radial out to see if the orbit line decreases after the slingshot when it's in front of Jool. You can use the maneuver node many days before entering Jool to see if Tylo will be at the correct spot to meet. If this isn't the case you should create a maneuver node so you arrive at Jool sooner or later so that you'll meet Tylo at the correct spot. In any case Tylo could be on the other side of Jool at the time of entering so you should plan ahead that way.
What do you mean?
In the KSP settings there's a conic patch limit slider. Each number past 1 presents another calculated orbit line. So that would be Duna <> Ike but nothing else. If it were 3 you could see Dres if that were your next destination.
 
The point is to use as much fuel to make a 2/3 resonance outside of Kerbin to meet back with Kerbin to rise the Ap above the sun. You have to match orbital time period 1.5x that around the sun compared to Kerbin to meet it back two orbits around the sun. You should use Better timewarp mod. It could then slingshot you to Duna to get to Dres for very little fuel and plane change also but you'll have to calculate ahead to see if Duna is at the right place.
Here's Mark Thrimm's trip To Dress using the Kerbin <> Duna Gravity assist after refueling his SSTO at Minmus.
 

I lol at that.
I have found that 1 Shock cone intake can easily feed at least 3.5 Rapier's but possibly at least a little bit more.
More intakes generally are necessary when you are rolling slow when a plane is heavy and there's not enough intake speed to further feed the engines. Sometimes more intakes are necessary when creating VTOL air/spaceplanes. Sometimes you only have one attachment node and one stack and you need more intake then 1 i.e. shock cone then you'd want a precooler or nacelle on top of that but only then.
I'm not sure why people combine precoolers and shock cones these days, unless the precoolers themselves are attachment points and fuel tanks are to heavy.
I also just made a low tech juno SSTO that can reach 70-500km orbit which has 8 junos and only 2 circular intakes and can reach 600+ m/s.
Front.

back.

@Klapaucius When I see the Navball it seems your pointing to 180 degrees (south)
But your plane is pointed east (90 degrees) on the runway.
So it seems your commanding the ship from a command pod or probe core that is situated to the south. My bet is that it is one of the cupolas as the navball also points up while the cupola module does also.
In that case Roll command Elevons will not know what to do as they will assume your nose is at the south but they're rotated 90 degrees from that direction.
Of course the solution is to "command from here" on a part that faces east like the Mk2 cockpit.