Rafts ... also run you over in surf waves and have they have no regard for eddying out for play spots
Sounds like you're boating with the wrong rafters. Everyone's got to be flexible for the whole group to get what they came to the river for. If I'm running with kayakers I'm happy to eddy out at a primo play spot, kick back, and enjoy the show.
More inportantly, thanks for analysis - there's a lot of good stuff here and I especially appreciate the part on run order for safety kayakers. From what you've said, I think the way to do it well would be after significant rapids, rafts eddy out if possible, or at least try to slow down, and let the kayaker(s) regain the lead.
Glad you made it out,