The track is all in for the lower level. Splicing the ME code 55 bridge track into the Peco pseudo-55 turned out to be remarkably easy. Per your recommendations I simply ground away the lower web of the Peco rail and the joiners slip right on!
Now I'm just wiring everything up. Plenty of feeders. Plus all the sidings (the two parallel tracks and the three yard tracks) are powered independently using rocker switches on the front of the layout. I'm running DC for this rather than DCC and the ability to store extra locomotives and whole trains during a show was a key design parameter.