I think it's super great that someone is willing to give some love to the levels. They're fairly bug free, but a little polish could help a lot in some areas.
The Abandonware version of Amulets and Armor uses the
additional skyboxes that are unused in the current "classic" release. Either the classic version uses levels that weren't completely up to date, or the abandonware levels got some love from somebody. Having played through both, I know of very few differences between them. Either way, I think assigning the unused skyboxes to the fixed levels would be a great improvement to atmosphere.
I kinda think that the "dormant secret area in Q3M1" was originally intended to be an alternate exit, one that you had to find in order to move on to the next mission. IIRC (off the top of my head) the exit text says something about a hidden connecting pathway to another barbarian clan that hadn't been used in years. I think there's another level like this in the Elmore Quest as well where you have to find the correct exit, as more than one exists. Though I could be mis-remembering.
I think that there are a number of unused text scrolls that are either unaccessable or not placed in the levels. I think re-integrating this lore by placing them or making them available would be good.
Also, as annoying as the acid is, I'm not inclined to provide immunity to it. It's a huge challenge to the game and speaks to the brutal nature of A&A. It's a hard game at times, which leads to a serious temptation to change that. I wouldn't be opposed to providing some potions or scrolls that would provide some temporary immunity though, so long as they're limited in supply.