You were right, I had "Request Sample Rate" checked in Reaper and it was set to 48k in preferences. If I un-check that everything works regardless of the project sample rate.
Edited to add I got all the Sonitus stuff working. For some reason Reaper wasn't seeing the compressor, or the gate, and put the delay in an instrument folder. Probably because it thinks the delay is a tempo based effect since you can sync it to the host tempo. I had to modify one of the .ini files to get the other two to show-up but all good now.
As for MIDI, the only issue I'm having is with multi timbrel synths like Kontakt. If I have several instruments in one instance of Kontakt I have to go through and route the MIDI tracks to correspond to the correct MIDI channels. Not a big deal, and if anything it helped me understand how Reaper handles synths in that manner.