[Edit: oops! I didn't notice this thread had a second page at first. Still, I'll leave my comments below for consideration. Not sure if you have the space to run the left end of the main into staging, but it would help with point #2 below.]
On the revised drawing, it looks like your A/D track will barely fit four cars w/o fouling the mainline or the switcher access. You can do two things to have longer trains on the A/D track:
1. Shift the switcher access to the A/D track (I don't know what the term is) further to the right by "cheating" on the yard ladder angle. In other words, if you're using #6 turnouts on the yard, build the ladder on a #5 angle using short pieces of ever-so-slightly curved track between the turnouts. This will shift the turnout leading to the A/D track a little to the right and allow more car space on the A/D track.
2. Move the turnout going from the main to the A/D track further to the left to squeeze a bit more room on the A/D track. You could even model the A/D track going straight off the layout parallel to the main - the turnout would be modeled off-scene in staging (or not modeled, but assumed to be there).