If you are running your DR-680, the pres in it are fine. I don't think people have many complaints about them.
If you want a smaller recorder for all-in-one, I have been running the Roland R-26 and find the preamps to be good. It also has a very good, clear display, easy level adjustments for the analog inputs, and solid battery life. And it's less than half the size of your 680. The R-26 has XLR line-ins so you can run the CM3s straight into it.
As to mics, I haven't done the type of recording you are doing, so I may not be the best person to ask, but I would think you want some omnidirectional mics to pick up the full feel of the ambient environments you are in, if I read you correctly. For that, it is hard to go wrong with something like the Countryman B3 (about $350 and needs to be wired up by someone, runs off plug-in power and doesn't need phantom), Nevaton MCE400 (a bit hard to find) or DPA 4060 (much more expensive, but quite easy to find).
If your CM3s are omnidirectional, I don't see any reason not to use them.
It would be helpful to know your budget, and exactly what you're hoping to use the recordings for.