The *original* release of M1A1 contained major modifications to the game data, but the Aleph One 1.0 release removes *all* of the major modifications – even the much-reviled “Colony Ship” puzzle has been reverted to its original status. Aleph One 1.0 is as close as you could realistically get to Marathon 1 using the Marathon 2 file format.* If you enjoy doing all this stuff yourself, that’s great, but I don’t really see the point in repeating work others have done unless you feel like you’re learning something by doing it yourself that you couldn’t have learnt more easily in some other fashion. The Aleph One 1.0 files should be fine for the purposes you have in mind, unless I’ve misconstrued something or you haven’t spelled out some of your end goals.
As for exporting the textures with OBJ files, perhaps you can ask about adding that to Weland (or, if you have sufficient programming knowledge, write it yourself – since Weland is GPL, the source code is publicly available for anyone to modify). Most of these features were just added because someone wanted them. The custom grid function was added by one dude who just submitted the code for it and then disappeared.
I still don’t really understand why you’re using OBJs rather than trying to get Unity to read the original game data, though. Is it just flat-out impossible to adapt MUnity or Forge+ to work using stencil buffer portals? I haven’t looked that closely into how any of this works, mostly because I’m busy with a bunch of projects of my own, but it seems like it’d be less frustrating to adapt one of those projects so it can handle 5D space with the original Marathon 2-format files, rather than redoing all of this from scratch, unless it’s just flat-out impossible for the code base of Forge+/MUnity to handle stencil buffer portals.
*At least, it’s as close as you can get without employing M1-exclusives like glue triggers and ouch polygons, but it doesn’t sound like those are what you’re concerned about, and the glue triggers are high-level game behaviour that probably only even matters if you’ve got both M1 and M2 monster behaviour replicated accurately in Unity. And those polygon types aren’t available in M2 maps, anyway – they’ve been reintroduced into more recent versions of Aleph One.
