Some more on the micro stutter
When you trigger whatever will start it, it will be happening everytime at max acceleration time, even on short flight, even when landed somewhere.
But if you jump into another system, the micro stutter will stop, even if you jump back in the system you were in.
I don't play Kerbal so i don't know how flight planning work in it, but in current version of Pioneer you select a target (planet/station/city/floating object/system) from either the view (if you see the object) or from the star maps (if on mission you can even set the mission goal to be the target directly), it will be listed on the left of your central reticule.
You will then be able to right click on it and select to autopilot to there (vicinity, high orbit, low orbit) or ask for docking permission or autodock.
I found that selecting autodock is a bad idea though if you ship isn't yet in vicinity of the target, the autopilot killed my ship several time this way.
It is also possible to try to go travel to your destination manually instead of autopilot , but you'l obviously have to do yourself all the mid flight correction, and manage your reactor correctly to not overshoot or crash into your target.
What is unknown to me is if the autopilot do its best at fuel management or if you would do much better going manually.
edit :
While on a mission to another system, i first jumped on Barnard's Star (as with the class 1 hyperdrive i took , i can't jump to the other system directly, too far) and a couple of space cops ships were right nearby and scanned my cargo (fortunately for me nothing illegal in the system) .
Then as they were flying in stragith line, i used my
good old Orbiter reflexes to actually try to get very close to them and match their direction to take a screenshot.
It's helped a lot by all the indications on the screen, as you can see the target ship vector, its prograde and retrograde pointer so you can match them better.
Though you need some very soft push on each directionnal reactor buttons when adjusting to not overshoot or collide
edit 2 : beware of the systems that actually contain multiple solar systems inside, because when you jump the game usually try to put you +/- in the middle of a system, but in the case of those special systems, it seems the game put you between all those solar system, so in the case i just got (in one of those Gliese with numbers named systems) my ship was at 75AU from any closest target.
And at max acceleration time it still take a lot of time to travel such distance.