I saw this thread a while back and found that these problems are easily solved.
I replaced my evap last week, which required me to remove the dash. Actually, I replaced the entire, dash as I am converting my interior from ivory to black. The replacement dash had alignment issues with the door panel, at least initially.
Turns out there is a simple alignment process: The height and inset of the dash is controlled by two metal brackets that holds the heater ducting.
The passenger seems to be afflicted with height issues, a 10mm open-end wrench can get fair access to the bracket from underneath. Loosen the two bolts, align and re-tighten. Back to perfect.
The driver side seems to be afflicted with left vs right issues. It is a bit harder as the fuse box denies access to the bracket bolts. A persistent tech can probably get access from removing the vent cover and the two 8mm bolts that hold the duct to the bracket.
You can also get a little bit of movement from the two black bolts behind the hard plastic vent covers.
I didn't have to deal with access because I already had the dash removed and just trial fitted it a few times. The problem is that you leave a gap at the inside A-pillar cover if you try and exactly match the inside of the driver door panel.
I suspect the dashes that are horribly misaligned are from a rushed evaporator replacement. I can see why they get $3k for the job and I would never hire it out as there are just too many things that can go wrong or have too many spare parts/fasteners left over.
Drew