I added some bridges to the roads crossing the rail lines, moved your rail cargo hubs off of the round-a-bouts and main roads. They are now in pretty much the same locations, but have a frontage road for their traffic. I also fixed three of your highway interestections and then cleaned up the lane mathematics. I let it run for awhile and you are now getting about 83% - 88% traffic flow depending on if it is rush hour or not. Enjoy!