Make sure you don't have a hole in cage at end where the chopper is. We had one and kept getting a bunch of cob pieces when doing corn. It would grind the straw pretty good too. Take off side under unloader auger and look in.
The biggest thing we have found in oats to prevent straw from being chewed up is to keep the beast FED! Keep it running at full capacity - the new straw coming in pushes the old straw through. That, and getting rid of reverse bars.
Did you install the green stem helical kit when you stacked the helicalsIJ That kit includes some extra helicals for thresher side and three helicals the hook up the thresher helicals to the angle of the seperator helicals. Be sure chopper blades are in good enough condition to suck straw from rotor. If machine has a discharge beater in place of chopper be sure it is doing the job. I'm wondering if you realy have a straw overload on chaffer. If your having any shoe problem it is 9 out of 10 times the condition of accelerator rolls.