Forgive me if I'm wrong, but I think you might be missing something (or more likely I haven't explained it properly).

I'll let you know how I think this works, and you can tell me where I'm missing the boat.

With this code, Pin A.6/Clkout is putting out a 1Mhz stream.
With the selected prescale, the interrupt will fire on every 4096 ticks of the main clock.
When the interrupt fires, it sets port B.7 high, then low.

Effectively, this gives me a 1Mhz signal on A.6, and a 244Hz signal on B.7.

I'm not trying to generate the "fast" signal, as that's done by Clkout. I'm just trying to generate the "slow" signal.

Do I have this right?

My apologies for the poor explanations.