Necroing this a bit, but I've just made my way through this level. It's absolutely impressive from the technical point of view, but playing it does feel a bit like a chore - so I love it as a fellow level designer, but hate it as a player
However, all in all I think this was definitely worth the effort!
The initial fight was quite challenging, but not over the top difficult. Shooting the first battlelord with shotgun/chaingun was a bit tedious. And I'd definitely change the assault captains in the underwater parts, because (1) they tend to disappear and never come back, as you mentioned in the .txt and (2) they don't even attack the player in the underwater sectors, so they're just there to eat some ammo and slow you down. Maybe using octabrains (and less of them) would work better, or even sharks. In general, I felt that besides the initial fight, the combat kinda just was there.
I didn't find the puzzles too difficult, only in the building where there were buttons in the basement and above the ground it was going too far IMO, as it was quite difficult to make head and toes of the hint for the basement part because it was symmetrical. Other than that, I thought the hints worked well and I'm glad there was plenty of scuba provided. Found all the secrets, although had to do quite a massive search for a few - particularly the 3 ones without any visual hint. The interiors of the buildings felt too cramped and a bit too repetitive, maybe having less rooms that are bigger would have worked well, but it's not a super big issue.
I have no idea about the original SM64 level, but this one was a technical marvel IMO. Of course, the pristine use of TROR with all the different planes worked well, the map looked good in Polymost and there were only a few rendering issues, I think you would be able to mitigate them by dividing the bunches at each wall. The small thing that impressed me the most was the TROR "enclave" near the switch that enables the arrow lifts, looking at it on Mapster I realised it's 2 sloped triangles that make it work, it is a bit buggy, but nevertheless I've never seen something like this done before. The large crack opening through the entire map towards the end was also really cool and I like how you even added a sunlight coming in. The viewscreen messages were hilarious, I appreciate the dedication to write them, despite in the end they mostly turned to be world building rather than anything useful most of the time (besides the hints to keep near the wall when falling). Despite all of the puzzles, the progression was very clear. There was one bug (I played in r10454) where at some point, the shrinker in the logic "machine" would stopped working for some reason, preventing the opening of the gates after pressing all the emergency buttons. I've tried with multiple saves to pinpoint the issue, but didn't found any reason why it would do that - I suspect it has something to do with jumping on top of the roof with the liztroops then going for the devastator secret, as it always happened after I'd do this, but can't be sure. Pretty annoying, but the jank can be expected with this level of technicality involved.
Nevertheless, I'm looking forward now to trying your other Mario maps!