I don't think I've seen a discussion with details about the PC-98 port's data, so let's begin here.
Unfortunately, I don't think I have much to say on the EXE. UNP 4.11 reports that WOLF98.EXE was processed with "LINK V3.69 /EXEPACK", and can unpack the EXE, although the difference in filesize isn't significant (271076 vs 272704 bytes). It does look like this EXE consists of 32-bit code made with WATCOM C/C++. A seemingly obscure DOS extender named DX386 was apparently used. That's all I think I'll write on the EXE for now.
Let's move on to the game data. The maps (GAMEMAPS.WL6 and MAPHEAD.WL6) are exactly the same as in the original GT release (1993), as well as the Activision release, so not much to say here.
As for the audio, IIRC 3-4 tracks were effectively removed (although there's still data in AUDIOT.WL6), while one of them (the one played in E1M4) was cut in the middle. Note that AUDIOHED.WL6 wasn't modified *at all*, compared to the same GT and Activision releases. So it feels like manual hex editing. I think I'll let you figure out the exact differences on your own, heh.
Things get more complicated with the graphics. It looks like *two* sets of graphics files are used by WOLF98.EXE: VGAGRAPH.WL6+VGADICT.WL6+VGAHEAD.WL6, and 98GRAPH.WL6+98DICT.WL6+98HEAD.WL6. Some hacks were required for exporting the 98GRAPH.WL6 data.
I should probably mention here, that there's been an xGAGRAPH importer/exporter floating around, known as ModId. This is a modification of LModkeen 2 (which in turn is based on ModKeen). Among other changes, ModId added support for CGAGRAPH and VGAGRAPH importing/exporting (only EGAGRAPH files were originally supported).
Note that I haven't uploaded a Windows EXE for now, but MinGW can be used to build one. You do *not* need to link to ncurses for the Windows EXE.
- The first two pictures are missing.
- The credits screen (wl6_pic_0084.bmp in the exported PC-98 port's data) is the same as in the last registered Apogee release (Apogee is credited for distribution).
- The various "ENDART" texts are also the same as in the Apogee release. Among other things, this includes the mentions of the "Read Me" choice in the menu and Apogee's older phone number. Note that this also applies to episode 6's ENDART, even though it doesn't have actual Apogee-related information.
- A partial pictures table (chunk no. 0), fonts and unmasked pictures are all that's present in 98GRAPH.WL6.
- The table chunk (no. 0), as well as the 10 HelpScreens pictures, are *not* Huffman-compressed.
- Chunk no. 0 has the *wrong* expanded size in the first 4 bytes. On the other hand, the HelpScreens pictures' chunks do *not* begin with the (common) expanded size of 320x200 bytes, but it should be clear what it is (since the pics are not compressed).
- Chunk no. 0 is also missing the dimensions of a few HUD pictures. This includes the last HUD face pics, as well as a few of the HUD digit pics.
- Furthermore, the HelpScreens pics' pixels are arranged in LINEAR orders, rather than planar as suited for that VGA mode.
WDC has a hidden "View 98GRAPH" option that only appears on the project information screen when the 98GRAPH files are detected.
Checking it shows you the chunks from 98GRAPH instead of those in VGAGRAPH and the last chunk it shows is one of the face pictures at chunk 145, which seems to match what you describe.
All of this matches what you've described.
Episode 6 - A masterpiece in design!