Ah, I am playing tekkit lite which doesn't include gregtech, and therefore no thorium.
I am beginning to speculate that my issues may stem from the compass orientation of the entire system vis a vis the order in which machines "fire off" in a single tick. In other words, depending on whether the setup is oriented east-west versus north-south may be having some effect on whether the sorter (pulling the damaged vent out of the reactor) versus the relay (pushing a cooled vent into the reactor) "fires" first in a single tick. If the relay fires first, it finds a full reactor and does nothing since the sorter hasn't pulled a damaged vent out yet. Then, the relay pops the cooled vent in on the next tick (meaning that reactor has to shut down for a tick every time this happens, and it actually gets worse because you're dealing with 8 vents, so it has to shut down even longer to replace them all) Ultimately, in this scenario it winds up shutting down 3 ticks for every 4, aka running at 25% what it should. This explains why my eu/t measured over several ticks seemed to be about 25% of what it should be.
On the other hand, if the sorter fired first, the damaged vent is pulled out, and when the relay fires it is able to pop the cooled vent in on the same tick, so the reactor does not have to shut down.
As I said, I think the difference here may be related to the orientation of the setup relative to the world. I will do some testing and get back to you.
I tested this and confirmed it!
Here is a screenshot of the test setup:
As you can see, I am facing north. The two setups pictured are indentical except they are mirrored. The one that is farther away/northernmost/closest to the top of the screenshot gets about 406 eu/t but the bottom one gets about 960 eu/t!!
There is a massive difference just based upon how the reactor is oriented relative to the world, so if anyone is having problems with this setup, this may be the culprit!
This is less important for reactors that get a longer cycle time (such as thorium), but even then it could get you slightly better performance due to needing only one rather than two tick to swap out the components.