MaximDL has a reasonably good bloom removal tool - not sure why you didn't use it.

You'll need to remove the bloom on each sub before registration and combine. This can be scripted using MaximDL's scripting capabilities to simplify/automate the process. If you've got a lot of subs, its worth scripting.
The typical muted colours of an LRGB are present. Try layering the luminance at 50% opacity first, then boosting colour saturation either using saturation controls or shadow/highlight tool. Flatten the image, then relayer the luminance at 100% opacity to get full resolution. Thus the image becomes a LLRGB composite. There are many other processing tricks to manage resolution and not sacrifice colours.
Look forward to seeing more.