2: I agree, but I didn't want to change the proportions of the geometry too much to fix that.
Those columns are connected to the iron bars of the ceiling, and the fireplaces are centered between both columns, so to fix that I'd have to move the fireplaces and change the relative proportions of the wooden areas of the ceiling. But I'll play around with the proportions to see which looks better: extending the transom, or shortening it.
1: The thing is, the design of the original doorway from the main hall to the episode 2 corridor is almost impossible to salvage:
screenshot. It was likely supposed to represent a toroidal arch, but Quake's BSP format doesn't support the kind of texture projection that would be needed to perfectly align the texture on all edges of such a thing.
So, I decided to reshape it using a mix of curves and square angles, keeping the textures continuous along the curves, and changing them along the square angled edges. With that in mind, I've also shaped it in a way that allowed most of the doorway to retain the original texture.
I'm not sure what you mean by the trim not fitting the width of the brickwork, but its proportions are exactly the same of the original doorway. In the original, the tiles in the lower steps were also cut in half by the doorway. There's no way to fix that without making the tile alignment change across steps, and I don't have a better idea.
There's a great challenge in trying to figure out what exactly some of the geometry in the original maps are supposed to represent. Trying to achieve a clear representation without deviating too much from the original design is a really interesting exercise.
The area where I took the greatest liberty was the path to Shub-Niggurath's Pit. The original was just a bland underground corridor with the same texture everywhere, but I thought that turning it into a proper underground cave would be more fitting. I've added wooden beams to make the steps of the staircase more noticeable, used a darker texture in the inside of the cave to give it a heavier atmosphere, emphasizing its "hidden underground" nature, and made the shape of the cave start wide and short, and end thin and tall, to emphasize the transition from the realm of humans to the realm of an elder goddess. I've also raised the ceiling of the room with the portal to Shub-Niggurath's Pit to put it in pitch black darkness, thus matching the ceiling of Shub-Niggurath's room in the end map.