The console I/O also seems to be dependent on external hardware to delay until the last character has been actually sent, or maybe your prototype was clocked slow enough that this wasn't necessary?
So, if the external data bus is always 24 trits, however addressing is in units of 6 trits, how does the hardware (CPU->memory interface) handle that? Is the address bus using binary instead of ternary?
What I meant by "conventional" is that other than using base 3, it isn't that different from other computer architectures, certainly not the idea you describe in the OP (that must have come later, since it isn't mentioned at all on your website). Some ternary operations might be useful for neural nets, but that wouldn't be an application for a general-purpose processor like this.
And some of the "messiness" might have been fixed, but again, there is absolutely no specification of what this architecture is supposed to be, so I was going from the one snippet of code that you have made public. And maybe you're still making changes, or do you intend to market a commercial microprocessor with absolutely no published specification?