How many miles have you ridden so far on the CT? I did the MERA 10-n-10 Rally in '10 and was riding 20 hour days for that rally. I never noticed any issues with the CT, in the later days of the rally, and had been riding on the CT for about 7 months at the time. I don't recall how many miles that ways, but somewhere over 20k easily. I did DNF, but it was for time barred, having made errors in planning that put me in Key West 29 hours before the mid rally checkpoint. That stretch had started in Tallahassee earlier in the day and turned into a 54 hour day, but I made it to the checkpoint with 15 minutes to spare. Couldn't recover from the sleep deprivation for the remaining rally days though.
If you're not thinking about the CT handling now, just responding to it w/o thinking about it, you'll do fine on the third leg. You get better sleep on the road than at the checkpoints anyway.
My IBR was not as intense as the 10-n-10 in terms of riding or length of time in the saddle each day. But the IBR was on the Super Tenere with Heidenau K60 Scouts, so I could have done the rally on one set of tires, but not knowing what the third leg would bring, I shipped a tire out and did a swap for the third leg.