2. Thanks!

One thing I may need to be more clear on based on some of your thoughts:
The monsters are generally meant to still "appear" as described in the adventure.
The replacement creatures are meant to be used as reskins.

3. The modron was selected because it was the same CR as the Tomb Mote, also had
multiple attacks, and had a gas attack to stand in for the Mote's disease attack.
For the most part, when I wrote something like, "Tomb Mote, use Modron Pentadrone
(MM226)" it means that the Tomb Mote is still a tomb mote but uses the other
monster's stat block as a proxy. The gas attack also helps it be a "solo" monster
by tying up some of the PCs and attacking with advantage on its next turn (if it
survives that long). You will find that the solos in this adventure get chewed up
and spit out in 5e (especially if you have a monk with stunning strike). So any
special stuff like this really helps.

4. The skeletons on their own match the challenge rating for the encounter.
Encounter Level does not exist in 5e, but my understanding is that it meant a
medium encounter in 3.5 for a party of 4 adventurers of that level. So what I did
was use that as a determination of how difficult to make encounters in 5e. This
allows some encounters to be easy, medium, hard, and deadly. By this point, the
party should be level 2. The encounter level for this encounter is EL 1. By making
a medium encounter for a level 1 party, it becomes an easy encounter for a level 2
party (just the way the encounter budget works). Giving the skeletons poison arrows
would up their CR and make this an EL 2 encounter. So I did not bother with it.
Generally, if I mention something in my conversion (such as a monster), it is a
replacement for what is in the text. So the skeleton in the MM replaces the
skeleton in the adventure and does not have poison arrows.

5. The skeleton is CR 1/4. The zombies are each CR 1/4. Filge is CR 3 (as he is in
the adventure). This makes an EL 5 encounter (as it is in the adventure): a medium
encounter for a level 5 party. However the party is probably level 2 (by milestone)
or maybe level 3 (by xp) by now. This is a deadly encounter for a level 2 party.
Making all the zombies the same fits in the 5e ethos of streamlining the combat.
There is nothing stopping those zombies from still being troglodytes and bugbear
zombies story wise, but the different stat blocks are unnecessary. The DM is the
only one who would ever even know they were different. Also, since Filge is CR 3,
the CR 1/4 monsters are the only things that fit in the encounter budget.