Neutering will help with the aggression and marking. In the meantime, you should get a Belly Band.
The car situation, not sure you will break that, some dogs just have pure fear and anxiety over car rides.
Also, SHE is HIS Momma, you won't be able to break that habit either.
As time goes by, things should get better, but alot of dogs go into a depression when their Mommas are gone
