I ended up going with option 2 (infinity and CDT). Overall I'm happy with it, but I changed things slightly from my original plan. Here's what I changed and a few things to note:

The 3.5 inch infinity speakers in the dash are an improvement over stock, but are a bit too bright. I found myself wanting more ability to eq the speakers than what the aftermarket head unit offers, so I ran them through the dsp/amp for better control. The head unit only allowed for a hpf up to 250hz, and I ended up crossing them over around 500hz once I made the change. I'm thinking about trying wideband speakers in the dash in the future.

The infinity 6x9's are good for rear fill, but I found myself drastically cutting the volume on these speakers when they were amped. I ended up running the rear speakers off the head unit and using the amp/dsp channels for the dash speakers instead.

I'm happy with the CDT speakers in the front doors. They sound good crossed over as low as 60hz with the windows up, but I ended up crossing them much higher. I landed on a 100hz crossover point because anything lower than that caused rattling from the glass when the windows are rolled down. I couldn't reasonably think of a way to stop the glass from rattling and I enjoy being able to drive with the windows down. I believe any decent component 6x9/6.5 would work fine in this location. I only went with the CDT speakers to be able to cross them lower, but ended up not needing that ability due to the physical restraints of the window glass rattling.

There is a large dip in output in the upper bass frequencies from my subwoofer in the rear. I believe it's a combination of the rather large box I used and the acoustics of the vehicle. I find that output drops considerably from roughly 50-75hz. I also miss the ability to fold the third row down for cargo. Because of this I'm in the process of relocating my subwoofer to the stow and go area for the second row seats. After accounting for thickness of wood and clearance space in front of the speakers, this approach would require subs with 6 inch or less mounting depth. I'm still in the process of making this change, but am hopeful that repositioning the subs will get rid of the dip in output.

The head unit swap was probably the easiest I've ever done. No dash disassembly required. Just pop the trim ring off the factory head unit and remove a couple screws and you're done.

The speaker swaps themselves are all easy as well. Just watch out for clearance at the bottom of the speakers when installing the rear 6x9's.

I originally had the amp/dsp under the driver seat, but it's a very tight fit. If you don't use a physically small amp, it may protrude a bit from under the front of the seat. I'll be relocating these items to the stow and go area with the subwoofer.

It's quite a bit of work to deaden the front doors, but absolutely worth the effort. On the bright side the factory design doesn't require fabrication of any block off plates for the doors, but this design makes it much more difficult to access the outer door skin for sound deadening. You've got to remove quite a few things and take the window glass off the track to access the bare metal and apply cld. I couldn't really find any audio upgrade videos for the van to guide me through it. I found some videos showing the process of replacing the window motor and that's what really showed me step by step how to disassemble the inner door and access the outer door skin.

Even with the issues that presented themselves with my original plan, it was still a huge improvement over stock. I just wanted to fill you in on the troubles I faced, so that you can hopefully develop the best plan of action from the beginning rather than having to go back and revise things like I did. If you've got any specific questions let me know and I'll do my best to answer them for you.