I worked at a Mr. Transmission for awhile and never really understood how we could turn a profit. Almost an entire day was spent rebuilding a transmission plus the remove/replace time to get it into and out of the vehicle. Then, add test driving and possibly removing/replacing it again if there are any issues.
This shop would NEVER upsell anything that was unrelated to tranmissions. I once had a vehicle in that had every single dash light on possible. I'm talking headlight warnings, TPMS, oil pressure ... you name it, it was on. I wrote this all up and recommended to the service adviser that we take a look at it. "Nope, that's another shop's issue. We do transmissions here. That's all we do."
If this shop made more than 10% net profit, I would be surprised.
Additionally, I did not know that a town of 12k could support a dedicated transmission shop. Maybe it can ... I do not know small markets too well, but it seems like a stretch.
Personally, I would do the following to increase revenue:
Start doing all vehicle repairs, not just transmission. Do a full courtesy check on each car. Recommend what you can, even tires. Heck, the car is going to be in there for a day or two anyway, so you can easily keep no inventory and wait on the parts/tires you need.
It may be more efficient to just buy a Jasper transmission off the shelf and send the core back ... rather than rebuilding every single one. This really depends on your volume, though.
It sounds like you are in a rural area. Have you looked into doing the big stuff? Tractor transmissions, Caterpillar work, etc? Lots of money to be made here, especially if nobody else is doing it.
Just throwing some ideas out for you. I wish you the absolute best.