You need to tuck those wires into a piece of loom after you heat shrink each wire. I can safely say I have 6-8 wires tucked under my brake booster as described above.
Out of sight, out of mind.
That's clean compared to the rest of the butchery! But yeah, gonna have to do something with them. The correctest answer would be to depin at the firewall if that's doable.