Replying here just in case anyone stumbles upon this some day.
My door card didn't fit back on after I added MLV and CCF. I took a few approaches.
1. Rubbed door card with colored chalk to see where it was causing issues on the MLV. - I cut down pieces of plastic on the door card that were the culprits - this got me 90% of the way there.
2. Heat gun - you have to be super careful with this one. It's worth testing it first to see how your plastic reacts. You can warm the plastic until its in a somewhat moldable state, but it won't neccesarily alter the appearance of the plastic. It takes a lot of patience and testing but I was able to bend/alter a few cupholders that were the main culprits of my doors not going back on. You can't really tell the difference by looking at it. I've turned Inny's into Outies to accomodate larger speakers or deeper speaker mounting brackets. It beat the sh** out of making a custom door panel.
3. Door clips! Dude ... this one was a game changer. I found that on my Honda, they make very similar yet slightly different door clips. Through NWCLIPS.com I was able to use their specs and find some door clips that were the exact same size, yet were a tiny bit wider in the middle of the clip - which thus gave them much better fastening power. I ended up changing out all of my door clips to these and essentially when I push them in, they don't come out. When I had to take my door back off, half of them broke off, the other half popped right out as normal (but with a little extra torque). Since they were around 25-40 cents each ... WELL WORTH IT!