I also stuffed them woth the left over foam from my headliner.
I would be very careful with the foam in the doors as this may soak up water and hold it causing Rust, internal sweating inside the door, also when wet it will make the door very heavy. Found this out when i did something similar in my old CJ5 ended up ripping out any foam or foam underlay as it seemed to attract water from every wear. Also it starts to smell.
Good job on everything else dynamat etc ,love the Soft top Idea for it to be insulated Like putting a coat on your jeep.