Ok, I managed to get a friend of mine to send me pics of the tweaks, he thinks I'm a total crazy son of a bitch. ;)

top: original below: tweaked

Boulder - 1st shot:

Boulder - 2nd shot:

see the left of the boulder... two more of the visible rod, taken from the trailer:

Well of the Souls - not the best pics and these are actually much easier to spot in motion as there's lightning (thunder), fire and movements that reveals reflections in these shots, but I marked the most obvious mark in the glass that was removed, if you look close enough you'll see additional scratches and marks that was removed below and to the right of the snake where Fords face earlier passes in the shot.

same mark removed in this shot...

For some reason they seem to be perfectly fine with leaving this shot alone:

For the tweaked Pan American Clipper matte shot, I found this one: http://www.caps-a-holic.com/hd_vergleiche/comparison.php?cap1=14343&cap2=14327&art=full&image=2&cID=1273&action=1&lossless=#vergleich

See the water reflections and removed matte lines. When the tweaks made are this subtle, I'm pretty sure there might be more of them...