Just finished listening to the whole thing. First let me preference this with that it was EXCELLENT. I've been working on a rearrangement/recording of FoA on-again, off-again for about a year myself, and I know firsthand how difficult this can be, and you did splendidly. Now I'm going to complain about stuff.
First, while I think that you succeeded in making the sound "more modern," I don't particularly think it fits an Indy adventure. Basically, I would compare it to trying to listen to Raiders with The Dark Knight soundtrack (extreme comparison, but it's what was in my head). While it's not inherently bad, I just don't think it particularly works.
Along with that, some of the mysteriousness of the original pieces I think is lost. Crab Raft is by far the best example of this, in which your arrangement of it perhaps gives a much more sinister sound to Atlantis, I think it loses a lot of its original, haunting quality.
That said, I think you did a much better job of capturing that in Lava Maze, though that song I always found a bit more 'sinister' than 'haunting' anyway.
The appearances of the Raiders March I think were the worst parts of the soundtrack, but mostly just because we've all heard live
recordings of it for years, and you can't really compare. The 'modern' sound hurts this the most though, with the percussion being entirely to heavy and drowning out the rest of the parts. It makes it feel as though it's dragging, too. Most of the 'action' cues seem like they're dragging a bit, in fact. Giving a bit lighter, but more driving percussion backing would help, or maybe even taking it up tempo slightly to make the cues more exciting.
What did you use to make it, by the way? I particularly like the strings and low brass you were using. Percussion sounded good, too, but I personally don't like it as heavy and thumpy. That might be the large amount of room noise you have set, though.
And again to end on a cheery note: Truly, a great job. Yes, there are other attempts at improving the sound of FoA, but you're clearly reigning at the top in my book for right now.