Very nicely done, that's truly brilliant work!!! There's so many jaw-dropping MOCs online that make the retail sets look like crap, but what you've done as a mod is stunning. I always prefer to see this kind of work, I feel less useless when I can be inspired by a clever mod. A mind-blowing MOC just reminds me of how poor my engineering skills are haha.
Anyway, my only personal recommendation would be to sort the front of the train out, it's so easy to make it just that little more more film-like with three trans-red 1x1 tiles and two 1x3 dark bluish grey tiles to give it a windscreen (I added trans-red grilles to each side too) that it's a shame not to give it that very simple facelift when you've done so much amazing work in making its architectural construction so much more screen-accurate.
Anyway, I too have made changes to the conveyex by combining two of them (was lucky to score them nearly half price in an amazon flash sale). However since it's for my boy to enjoy actually playing with on the floor, and not just old dad here tinkering with it haha, I extended it horizontally instead of vertically. Just having it look more like a proper train for me was a huge boost to its design. Now I stress this is still a work in progress, waiting on more plates to bulk up and provide texture to the front of the main drive engine, but for now you'll hopefully get the idea of where I'm going with it. I've turned it into a prisoner transport, since it's a delight to see how much room exists inside (so many Lego vehicles look so large on the outside but only have room for like two figures, so to have room for multiple troops, actual seats and prisoners was a delight). I've blocked up the visible holes on the locomotive's engine block (though still a work in progress, will have an actual engine in there in the near future) and added a second layer of black plates beneath the big drive "flap", thereby ridding it of those horrible flimsy see-through areas.
I've also filled out the cockpits to have them more industrial inside, with an Imperial Combat Driver on one side of each drive engine, with a Conveyex driver on the other side. These will be unveiled once further parts arrive. But for now, he's a peak of what I've been doing, hope you like what you see, more to follow when it's complete!