You usually do not need antivibration mounts with a Cube, they are better being hard-mounted unless you have absolutely no option.
Your wiring will be inducing vibrations, especially that spiral wrap, it’s not suitable for use near the flight controller. All wiring should be secured to the frame so it does not vibrate and move around, with just enough flexibility where it connects to the flight controller.
DO NOT fly again until you’ve taken positive steps to sort out the vibrations and tidy the wiring - the risk is you’ll have a fly-away or worse. Even considering the price of the props it’s not worth doing more flights until vibrations are greatly reduced and other configurations are improved (see below)
To fix the GPS start with these:
BRD_BOOT_DELAY,3000
GPS_GNSS_MODE,5
SERIAL3_PROTOCOL,-1
There is also a Here4 firmware update (do not update the UBLOX firmware!! ) , but this is probably not the cause of your GPS config errors.
You have a few parameters that are unsuitable for your copter - you’ll need to revisit the Initial Parameters calculator and start over there, selecting both “suggested” and “Flame” options.
The best way is to use the Methodic Configurator which will cover all of those and more.
In there will be a section running the VTOL QuickTune script - make sure you do that when you get to that stage.
Dont try and skip ahead through sections and go straight to Autotune again.