First off, hats off to Sitra Achara for an amazing mod. Not only can I play the game once more on Windows 10, but it works better and more faithfully to 3.5 than ever before. I started a new game a few days ago and am having a great time. I'm about half way through the Moathouse, having done the Deklo Grove and Emridy Meadows. I'll list off the potential issues I've come across so far (for the purpose of improving the mod, not criticism) and, once the forum clears my initial post, I can offer save games, if desired. Ordered categorically:
1.) Spider venom
Spider venom seems to be MUCH deadlier than it suggests in the help menu or in the source books (1d4 STR damage, twice, over a minute or so). In both my encounters with spiders thus far, though, one bite paralyzed characters with CONs of 15 and 10, respectively. The second time, the total damage amounted to a whopping 16 altogether, bringing them to -6 STR.
2. Holy water
A few small troubles with holy water: the SHIFT+Click description incorrectly gives damage as 1d6 instead of 2d4 (actual damage done is correct, however). Thrown holy water does not correctly count as a ranged touch attack (the target's armor bonus still applies). Holy water bottles do not break once thrown (allowing the party to reuse picked-up holy waters forever).
3. Heavy crossbows
Reloading heavy crossbows incorrectly takes 1 standard action instead of a full round (this was either a mistake or balance adjustment from the original game, I think).
4. Rapiers
The game incorrectly treats rapiers as a light weapon when wielded in the off hand (like short swords). They should be considered light for the purposes of Weapon Finesse, but not for dual wielding. The cutlass Brother Smyth sells in Hommlet is the correct version of the rapier.
5. Cleric's Protective Ward
Clerics with the Protection domain can use the Protective Ward ability. This grants +1 to saving throws per class level for 1 hour. However, it seems to be dispelled after any regular attack, even if no saving throw was rolled.
6. Magic thieves' tools
The thieves' tools outside the Moathouse claim to be magical when talking to vendors (and can be sold for around 30 gp before being identified, like any magic item), but, after spending the money to have them identified, reveal themselves to be ordinary thieves' tools.
7. Archers' five-foot step
Early enemy archers (the caravan bandits in the Lawful Good vignette and skeletons in Emridy Meadows) don't seem to take a five-foot step before firing their weapons, needlessly invoking attacks of opportunity. This could be a balance consideration: maybe the developers wanted to cut low-level parties a break? Maybe skeletons are too mindless to use such tactics? In any case, once the party reaches the Moathouse, enemies properly take five-foot steps or switch weapons.
8. Misaligned portraits
Hroth Renton (Elmo's dad, in the far south-west of Hommlet) has a portrait that does not align correctly in conversation--it appears far above the dialogue box at the top of the screen. Also, when tracking, monster portraits appear far below the pop-up box towards the bottom of the screen.
That's all I've found so far! I will write here again if I discover anything else of interest. Thank you so much again for your amazing work!