Hmmmm.....
Yes the box will work, a pound of fill in each side will add enough effective space to work.
You need to separate the 6X9s from the subs. I would suggest you use 1 of your amps for the subs, running in 2ohm stereo.
If front to rear fading is important, another amp is needed for the rear 6X9s.
You can run the front 6X9s and the 3.5s off the other amp with caps to filter out lows from the smaller speakers. If that isn't enough treble, the deck power (capped again) should be enough for those extra tweeters.
If you really want to power everything on amp power, which I like to do, it could be done several different ways.
For example, if you get another one of those same amps, you can can use 1 for the subs, 1 for the 6X9s (front and rear) and the third for the 3.5s and the tweeters. By putting the front outputs on the small speakers, the rears on the amp for the 2 pairs of 6X9s and the sub outs for the sub amp you should be able to adjust the sound levels to your liking. This setup also gets the most possible out of your amps, since they are all running in 2ohm stereo with the right frequency ranges for each type of speaker.
I'm sure others will have alternate ideas.....the van has a lot of possibilities and sounds like it should be a blast when it's all done.....
HTH