Okay, I think I have the menu code neatly encapsulated now.
You'd use something like this to trigger initial setup when starting a new game. It'll handle everything automatically, including a GameVariable to prevent triggering again when re-entering the level. Help boxes don't seem to display during cutscenes, so rather than doing this before the hub cutscene, I put this in script 0 for level 4 (the start of level 1).
ActorFactory.Spawn( "TurokPlusSetup", 0,0,0, 0 );
And I spawn an access point in the hub by adding this to script 0 for level 5. Naturally, you'd change the location and rotation to whatever suits your map.
kVec3 v( -1575-50, 4995, 972.8 );
ActorFactory.Spawn( "TurokPlusTerminal", v.x, v.y, v.z, Math::Deg2Rad(180),
Player.Actor().GetSectorIndexAtLocation(v) );
The spawns will silently fail if Turok+ isn't installed, so you should be able to safely add these to maps and mods to add Turok+ support without needing separate Turok+ versions of maps or map scripts.
I think all that's left to do now is to tie the settings to your save file.
edit: simplified initial setup even further with an obvious change I just realized.