I'm close to beating this, but here is some feedback from notes I have been taking
Answers to your questions,
1) My party is Max level (my Walking Dead party imported from beating the Main Campaign). Level 16 Mino Throw Barb; Level 17 Mino Alchemists with Heavy Weapons; Level 16 Lizard Alchemist Mage; Level 20 Farmer Mage. This might not help you, but I do make it a point to import my Walking Dead party in to every single Mod I play (unless the Mod doesn't let me do it). I like my party too much to start a new one, but your Mod does have a good replay factor; and the Throwing Barb in my group wasn't very effective here due to a small number of throwing weapons (I discuss again below). Instead a Light weapons Barb would have been much stronger in this Mod.
2) The food supply had to be rationed, but I don't think this is a problem since it was due to the fact that I take forever to solve puzzles. It looks like I can go fishing in the waters around each temple any time I want. I captured a few already but haven't tested to see if the waters replenish. If you aren't already doing so... you can consider a Timer or Trigger event that re-stocks these waters every so often with a small number of fish. I did allow my party to "starve" many times; but mostly because I was trying to solve these Math puzzles. Once I solved a puzzle I would let my party eat before I continued exploring. It all seems quite balanced in this regard though.
3) The boss battle with Ilius is the hardest, but the most fun for sure. I have not defeated him yet, I need to prep a little better first (I had zero potions when I walked in to his chamber). Nothing needs to be changed in Monster encounters in terms of difficulty. However, one thing I did notice is that in a lot of cases I ended up encountering a Snake, Mummy, and Medusa while their back was to me. And not just 2 or 3 times, I would say 90% of the time I walked in to a room or hallway and easily backstabbed most of these creatures within Underground locations. The above ground and open room fights were fine; but not hallways and small rooms. This isn't a problem necessarily, but it made the fights super easy since I was able to get all 4 Champions to attack before the monster even knew I was there. Granted my party is high-level, but even a level 1 party would have an easy time if most battles start off with the Monsters back to the group. Maybe consider monster blockers and triggers to help make sure the monsters have a stronger chance of facing the player?
4) The number of Herbs you placed is perfect, imo. And I love how the game unfolds in such a way that a whole lot of walking is required; yet the walking is short distances, quick, and easy - which means the player doesn't really feel like they are walking a lot. The end result of a great map layout throughout the game is... tons of herbs for my Alchemists without ever feeling like I was "pharming" the need to walk around. Time flies very well in your Mod.
Additional Feedback,
The Sanctum uses the Castle tile set, however, the Module Height needs to be set to 4 in order for it to display properly. Example of how this causes a strange effect, when I was in Elder Dena's room in the Hive, a secret door can be found by placing the Snail Figurine in his Castle Alcove. Yet the entire Alcove is not visible due to the Module Height; we just know that it is an Alcove because we played Grimrock and saw how Aclove's look in the Castle Tileset. Consider setting the Module Height to 4 on all Castle area's. This may not be entirely possible on single Maps with Multiple Tilesets, but a handful of areas can probably be improved upon.
I sitll need to defeat Ilius, but I can already tell that my Throwing Barb will have some trouble in the fight. There are not many throwing weapons to make him effective (unless I have missed their location?). I have only found 5 of 11 secret so far, but I am near the end of the game and I spent most of the time working with 2 throwing knives and 3 Shuriken. Only recently did I find 3 Throwing Axes. This worked fine up until I fought Ilius. Many of the throwing weapons stay "stuck" inside him until he is dead (as is normal) so more than half the fight my Throwing Barb will be forced to use melee weapons.
The Stone Puzzle that provides access to the Hives may have a slight bug in it. When I first encountered it, there was already a Teleporter visible. I took it and it went to a bedroom in the Hive. I marked its location on the Map but I did not mark the placement of the Stones. I don't think I ever found a clue to tell me how to get back here. It doesn't seem important but I kept wanting to re-visit that room; but unless I missed a clue, I would have to start a new game and document the Stone Placement. This isn't the bug, just wanted to mention this first.
After I found that first bedroom I saw the sign that gives the Access Key to the Mines. I completed that and moved on to other aspects of the game. I later returned to this location and entered in the access key to visit the 5 rooms listed in one of the notes (Elder Dena, etc). I went in order so when I was finished, the placement of the Stones was for Ka Flos (2,4,6,15,16). Again I left this area and finally returned again to work on the Snail Puzzle secret. When I returned the stones were still in the location for Ka Flos. I then moved everything but the last stone in order to provide the key for Elder Dena (1,3,4,7,16). The portal didn't come up. I assumed it was because I did not move the last stone; which could be a bug. The last stone shouldn't have to be moved since it was already on the 16 that both Ka Flos and Elder Dena share as a final key.
Now the part that really felt like a bug is when I moved the stone. My thought was to move the stone out of the 16 position and then back again. So I pushed it on to the 15 position... and then bam! The teleporter appeared for Elder Dena. Which means I was able to access Elder Dena's room with the key: 1,3,4,7,15. Nothing major but might want to review how this script and calculation is working.
Regarding the 3 color gems, I was able to solve this puzzle before finding the clue on how to solve it. I noticed that I was able to solve this puzzle by placing the gems in any order on the pedestals. It might be worthwhile to make it so that they have to be in a certain order (and the correct order can be detailed in that secret note that discusses the gems). As it stands now, I solved the puzzle before finding the note and when I found the note I read it hoping to see something about the order of the gems. It would have been cool if there was a specific order that revealed another secret!
The last thing I will mention is that in the Sanctum there are pressure plates on elevated platforms. Some of the pressure plates "flicker" which is something I am familiar with since I had the same thing happen in my Mod. If your problem is related to mine, you might have placed a Castle Pressure Plate on top of a Floor Tile. When this happens, that area glitches graphically. You may wanna check things and make sure there is only a Pressure Plate on top of either an Invisible Platform or a Void tileset.
That's all for now! Great work; I'm looking forward to beating the Mod tonight.
Glad you enjoyed the trick to get him out. Any ideas on how to make it more apparent to the player that it is possible?