I'm taking this as an invitation to dig deeper. I feel a bit lonely playing the adventure so many years later when everyone is done talking about it.
I'm back into D&D after a 20-year absence (skipped 3rd and 4th edition) so I'm having trouble adjusting to the new world of massive amounts of damage being dealt yet everything being less deadly in general. Your insight into how you designed the conversion really help.
1. My intent was to preserve the deadliness of the original adventure (I wanted to challenge my experienced players) but I ended up with a TPK and complaints that things were too deadly, often when I veered from your conversion.
2. I found the converted DC check logic (60-80% of the 3.5 version) a bit easy. My impression was that most people should not make the DC25 (now 19) check on Wind Duke glyphs but generally parties have at least one person proficient (and they likely have a high intelligence) so it seemed like 25% of the time the mage would know it all, and with multiple people checking, someone else might get lucky. DC11 trap checks and stuff seemed really easy. Nearly every check was made by someone, though possibly they just rolled lucky. The math is reasonable, but I have no experience with how hard these checks were in 3.5 so they read like they should be hard but were easy.
3. The TPK was at the Green Tunnel (7). I thought the Ankheg was out of flavour (no breath weapon in the original) - it felt like a better fit for the acid beetle cow (Giant Bombardier Beetle) in the hive (16). I used a home-made conversion from elsewhere on ENWorld:
Mad Slasher
Medium aberration, chaotic evil
Armour Class 15 (natural)
Hit Points 32 (5d8+10)
Speed 40 ft.
STR 13 (+1), DEX 17 (+3), CON 15 (+2), INT 6 (-2), WIS 10 (+0), CHA 6 (-2)
Senses darkvision 60 ft., passive Perception 10
Challenge 1 (200 XP)
ACTIONS
Multiattack. The mad slasher makes two melee attacks with its claws.
Claw. Melee Weapon Attack: +5 to hit, reach 5 ft., one target. Hit: 1d10+3 slashing damage.
...and between it and the swarms, the party was destroyed in melee and it was only the 2nd encounter! Oops.
4. I didn't use the spectator because it seemed so different. I see now that it was intended as re-skin, not a different creature. In hindsight, I'm embarrassed that I couldn't figure that our or just make the assumption. A spectator is a late encounter in the Phandalin intro module when characters are a high level so I was also worried it was just too deadly, and the option to smooth talk around the service contract isn't available if it just happens to be wandering around vs. being assigned to guard.
5. The Giant Centipede in 16 and 17 seemed too easy. 4hp and no range attack? This brings up the question of hp - in some places you indicate the hp, generally when it's injured or when it's non-standard, but in others you don't, so I assume I use the MM hp total not the adventure total. This became a bit confusing for the Owlbear at the Farmstead - it's supposed to be injured, but no alternate hp total is given. By that point, 2nd level characters against a single creature means it didn't fewer hp for the injury. Is that what you were thinking too?
6. The Water Weird in room 19 was incredibly deadly. I never let them attack it from the land, they had to go underwater and out of sight from the corridor. At that point it's invisible (immersed), they're holding their breath, only piercing weapons are effective (and it's resistant), they can't cast spells - it was a nightmare! I wasn't sure they'd be able to get through the encounter.
7. ...meanwhile the underwater Ghoul in 21, which is built up in the adventure, was a simple and forgettable combat. It seemed like the ghoul should have the same underwater disadvantages since it's not native to underwater (Lacedons aren't in 5e yet) so it was even easier as a result.
8. For the Ghost (23) I luckily managed to possess someone very early on. With a low 11AC and just 45 hp (though I kept switching between hp given in the module vs. MM defaults, now I know!) I was worried they'd fight and kill it!
9. The Owlbear was easy. I'm glad you mention the 300gp baby owlbear value vs. 3000gp, I had forgotten and was reminded right now (one of the players has adopted the baby).
10. Plot note - my players learned that the tattoo belonged to former miners from the old boss, but they then assumed that there were dozens of miners with the tattoo so it would be impossible to figure out which one was at the house digging up bodies. The module seems to assume that only Kullen's gang are left from that old mining company, but explicitly says that all the remaining miners work for Smenk so there are lots of suspects. This isn't something to address in the conversion, just something I'm curious about.
11. They didn't follow up on the Kullen angle but ended up finding their way to the Observatory directly (due to a random rumour roll). That was a bit disappointing as I'd prepared Kullen a bunch. You mention "1 CR 0-4 hoard" as random treasure on the gang. I rolled them ahead of time and got useful potions for the gang to use (plus a philter of love...which let me create a random side plot that is yet to be encountered). Did you consider rolling the treasure and giving them the magic items to use?
12. Merovinn Bask has a lot of hp too, like Filge. Heck, the Berserker has crazy hp. I'm having a lot of trouble getting used to HD not being relevant to level. The Bersker hits like a 1-3 level fighter (+5 to attack with 16 str) yet has 9HD. This seems internally inconsistent - players can never match the berserker's stats despite being a human fighter. BUT...that appears to be how things are designed. And it does make for better game play in that a 15hp solo wizard will get crushed, Mage Armor or not.
13. I thought the Tome Mote was intended as a trivial encounter. They are post-2nd edition so I have no experience with them (looked them up though). As you note, the modron re-skin was defeated in the 2nd round of combat. However, the players were lucky it rolled a low initiative as in it's single action it managed to hit 3 out of 5 times (one was critical) and knock one of them to 0. They were startled that something so dangerous was hiding in a closet! I didn't use the paralysis as I couldn't come up with a paralysis gas re-skin from an "accumulation of tomb litter", though I guess it could have been an unholy wind that paralyzes opponents with the voices of the dead or something.
14. By the way, I really like having the page number for each monster.
15. We stopped the last session just as the players are opening the door to the Observatory with the skeletons, finishing tonight. I had planned on adding the poison and sticking with crossbows, but I think I'll go with your more balanced design and give up on trying to re-create the exact same experience as the original.
16. With regard to four copies of Mage Armor...I just realized that I misunderstood the spell preparation rule for wizards. I thought they could prepare X spells of each level (so why just one 1st level spell prepared?), not overall. Wow. That changes things.
17. You increased him to 5th level which has a powerful effect on his cantrips. Chill Tough and Ray of Frost now do 2d8 damage. Was that intended? When I first posted, I didn't realize this so range attacks for d8 seemed pretty weenie. Now I can see that he doesn't need that many other spells. Heck, Melf's Acid Arrow is barely better.
18. I wasn't sure if Stinking Cloud would be a good idea since it obscures the battlefield and limits range attacks. On the other hand, it protects him from range attacks!
19. Ray of Enfeeblement seems really weak. Most people seem to use dex weapons (dex is so good!), so it's only effective against maybe one person and it requires both a to hit and concentration (as does Cloud, Fear and Vampiric Touch). This is just random commentary on the spell - Necromancers get no love at the lower levels!
20. I had forgotten about the Owl. I'll see what I can do with it.
21. I'm still deciding what to do with the Wind Warriors. The Internet was abuzz in 2006 about how deadly the combat is so I was going to go with another custom conversion, but you've changed my mind on encounter strength and I think I'll stick with the gargoyles you've suggested + some special abilities. My players thank you in advance!
22. I'm not sure if I'm going to do Chapter 2. The players aren't into the endless dungeon crawls (reviews weren't kind to Chapter 2 online) so I think I need to try something different. I was very excited by the Age of Worms based on the first adventure and it wasn't until after I started that I read the middle chapters and realized that it seems to be mostly dungeon after dungeon. I was hoping for more adventures based on the rich Diamond Lake background with mine managers doing political maneuvering and stuff, but that didn't come through. I like the overarching plot though and will likely try to use a few of the later chapters.