Electric noise issues in classic car
Ok, some time has passed by now and I got it working. I thought to share my modifications with you, so maybe somebody else in the future will find the answer for his/her problem here on this page.
The changes I made to the system:

Added a 2200uf capacitor before the buck/boost convertor (1000 uf probably would have been enough, but I had this one laying around and space wasn't a problem)
Added a 100 uf capacitor after the buck/boost convertor
Included an NTC resistor before the 2200 uf capacitor to limit the peak charging current during start charge of the 2200 uf capacitor to protect the fuse (maybe not necessary, but I had space for it)
Added a ferrite core clamp on the incoming and outgoing power line of the system
Changed my wiring from the rotary encoders to the raspberry Pi. Before I used seperate wires for all encoder pins and to limit the number of wires I combined all ground pins together near the rotary encoders so I would only have to run one ground wire back to the Pi. Now I used 0,5m long UTP network cables, which have twisted pairs. For each pin I used a seperate pair with one wire from the pair to the encoder pin and the other one connected to ground. So every pair has at least one ground wire. This should help to reduce interference. Near the Pi all ground wires are combined again and connected to the ground pin of the Pi. This change made the encoders work perfect, also with running engine and during driving.
Move all my music files from the USB to the micro SD of the Pi. There is also a bluetooth dongle connected to one of the other USB ports and apparently that can cause problems with continuous playback of the music when on the USB because of some internal limit inside the Pi. Removing the USB from the system as storage for the music files solved this problem.

I installed it all yesterday and had a great drive with a perfectly working music system. Life is good.
Thanks all for your time to help me out.