It was suggested in a comment on the previous post that I simulate the pump without a C60 molecule in the channel. The results are interesting.
Sure the rotor still comes apart, but now we have a better idea of what is causing it to. Ruling out the interaction with the C60 molecule, my hunch lies with the casing interface. Looking closely at where the rotor comes through the casing you can see that there is a potential for interference especially since I didn't craft anything like a bushing but instead merely chopped a hole through it as is often my MO.
I will touch this up and give the cnt design a final go before switching to the bar-rotor. My sincerest thanks goes out to Bleyddyn for looking a little deeper on this than I did.