Sorry to hear of your troubles.
I asked on the rme forum if the new usb-c MBP's work fine with my rme usb interface as was thinking of making the switch.
https://www.forum.rme-audio.de/viewtopic.php?id=24614
As you can read the rme moderator mentioned apple or intel need to sort out a basic usb-c issue and there was nothing they could do about it from their ( rme ) end. Some people seem to be doing fine with it and some have had more success with different brands or type of adapters ( ? ).
If you have reaper optimised in preferences ( audio>device>block size - e.g. not 13 samples whilst using many vsti's ? and audio>buffering>settings - not turned off anticipative fx or different auto / reading processing threads than recommended i.e. 4 for quad core ) and latest interface drivers ( do they support / are they compatible with latest apple OS ? Sierra ? ) and its not being caused by a 3rd party plugins ( ? ) then i fear it is on apples side. Hopefully an OS update will fix it but i am not sure a basic usb-c issue ( hardware ? ) can be resolved this way.
The usb-c problem needs resolving anyway so please let apple know ( the more people the better ) :
http://www.apple.com/feedback/ and go to genius bar or file a bug report.
and let us know how you get on.