eye issues happen with gars for some reason...we still haven't quite nailed that one down yet, but i have noticed with my own fish that the Cubans eyes stay clearest at higher pH than lower pH. i wouldn't really be too concerned with eye coloration as this fluctuates with gars and we haven't noticed a direct correlation between cloudiness and stress with these species.
as for the coloration change, it is hard to say. it's not as dark as the really stressed out Cubans in my experience, but it is a bit darker than usual. just keep an eye on her and go after that substrate. what is your filtration on the tank and how often do you change the water? when was your last water change?
as for lying on the ground...this is typical behavior with pretty much any gars at least at some point over the course of their day. i wouldn't be worried about that unless it looks like she's laying there and breathing really heavily.
i would make the substrate adjustments and provide more info on your maintenance, but overall i would expect that the fish will be fine--
--solomon