The issue I was having seemed to be related to the current Aleph One version at the time (1.4).
Tried said levels again with the Aleph One 1.5 release candidate, and they work fine now!
Overall, definitely a very good scenario for the M1 environment.
Here it is, at last: Marathon TROJAN. Now compatible with Aleph One (1.3 or newer), this uses the native M1 files to deliver the original, unaltered experience we know from the 90's.
M1 compatible fullscreen HUD plugins will work with TROJAN if you don't want to use the included Classic HUD plugin.
Additional files include the Weapons Pump Patch, FAQ, Manual, Spoiler Guide, and read me's from older versions of TROJAN.
Special thank you to Hamish Sanderson for giving us permission to distribute this re-release of TROJAN. Enjoy!
Update 3/3/25 - You can also find a Trojan standalone edition here https://hhas01.itch.io/trojan-se
"James’ Trojan AO scenario (2020) is a highly faithful warts-n-all port of the original M1 Trojan. This was important for historical preservation of early Marathon history, but not a great gameplay experience itself.
Trojan Standalone Edition (2021) made numerous fixes and enhancements to James’ scenario and customizations to the engine code. That’s why it’s released as Standalone Edition, not an add-on."