Hi,
Not sure if I’m an expert (it’s not mine to tell) but from the reading above I believe I could give you a hand with the issues mentionned.
May be for the glowlayer you could already take a quick look at this recent post (among others).
I also have xp with everything related to materials and lighting. I guess I could fix your colors and transparency issues. Although I don’t know about your expectations and the art direction.
Currently I’m working on a scene that is nearly all based on alpha blended materials. Here a couple of SS (wip). The env is not yet the correct env and most materials are WIP (but they are all custom, full PBR and from BJS only)
Let me know if you want me to have a look at it. In case, you can PM me.