hmm, despite an elaborate set up, the first set of renders are not that great.

what i think you should do is start with a single light [sun light] use s ingle point of interest. [even though you want to do different time of day renders, this will be a good starting point]
after deciding a god point of interest, try to get desscent result without GI or FG [so u get a good intensity to start with. as of now maya's light settings are not real world; like maxwell render]
then gradually add GI and FG,
when u get a good result and have gone as far as you can go with a single light [sun] light source, then add fill lights.
also remember that u can use blocking objects to emit light with MR.
also there are much better shader you can use to speed up FG irradiance shader
here are some cool test renders with a single light source Here


P.S. post your render settings as well.