Well I am glad I decided to stick with the Atlas turnouts instead of tearing everything up and replacing them with Pecos. Just had to add a couple of feeders in the proper place, do a bit more pavement trimming and now everything runs smoothly backwards and forwards. 

I also added a lot more weight to the boxcars to really give them some heft and also help them roll through the turnouts much better. Almost ready to move to the next section which does not include any tracks in the street. It does include a bridge, a canal and a major highway crossing. Fun, fun, fun.