Well you fold a towel and put on the top of the crate. 


When you get really good I can come over and you we can build a cage for my sub

I like it!
Good solution to the problem.
Any cage in a truck is gonna be a compromise and that's not even much of a compromise
Only nit pick I have is I would likely put a bar in your small rectangle. It will add strength but mostly cause I hate non diagonal shapes in cages

Can't sleep so you have my 3:34 am attention.
It's always hard to see what will work without looking at spaces and dimensions in person but here is my armchair quarterback suggestion on the roof.
May I humbly submit to you the idea of going full corner to corner with your main bars. Then horizontally V ing into that horizontal x node from your vertical V in the b pillar plane. Then come from that intersection with a single leg straight forward to an upside down V (with a smaller tube and spread for visibility) for the windshield bars tying into the dash bar i assume you'll have.
I shall call you cage, Asterisk *


Looks strong AS **** to me . . . but I like to build things that way![]()
Meh, notching won't be that bad, you got this. That program will generate paper templates too won't it?
just save all the pieces you notch out so you can weld them back in. Hehe