I took the guidance to heart and saw what I could do using O-42 as the only turn radius (aside from the trolley loop). I wish I could figure out how to do inclines and levels in SCARM so what you see is just a top-down view. I know it will be limiting but I only want enough vertical clearance on the tunnel portals to allow for the RTR PolEx with 1/2" clearance. That is to lessen the grades. The orange grade is essentially down only but hopefully allows for PolEx to run unattended using both loops (from bottom clockwise - lime green, teal, pink, orange, yellow, lime green, teal, etc.) while second train sits on floor level siding (lime green and yellow). Simultaneous two train ops (unattended) would have one on the upper loop (pink) and one on the lower loop (lime green and yellow).
I did end up with three slight disconnects but these are all about 1/4" so they should be made to work using just a bit of play. I've also provided the SCARM file in case someone can help with adding the inclines and upper level (all pink and purple).