body filler is made to smooth a surface, not to be caked on. you spread it on as thin as possible and sand it smooth.
pods should be built like bricks to stop that resonance. you can get fiberglass reinforced body filler and just smear it around inside the pod.
to seal the holes, if they are small, you could just use resin and pour it inside the pod.
as for the vinyl, some types are stretchier than others. but its all about how you pull. my 1st time went pretty bad lol. i had to watch someone do it. start in the middle and work your way out. you can come back to some wrinkles. get one curve close then move back and re-stretch the wrinkles. dont worry about pulling too hard. leave a lot of extra material for you to pull on, dont just cut it to length.
hope that helps.