*UPDATE*
Well it seems I've resolved both problems at once.
After I found the rock she ingested in the bottom of the tank I thought that was that but oh no, it couldn't possibly be that easy if Beaker is involved. This morning I fed them both pellets in a separate container to try to keep the water quality up in the 90 gallon. Both ate as usual, but then there was an inordinate amount of splashing and when I looked in Beaker was going crazy! Thrashing and bouncing around in the container while Gomie cowered in the corner. This continued as I picked her up and put her back in the tank. Then she began swimming like crazy all over the tank, bouncing off the walls. I left Gomez in the container, figuring she would want no part of this. Then Beaker suddenly stopped and grabbed hold of the edge of the basking ramp with her rear legs pulled in.
Then it happened. A huge cloud of green-brown stuff started flowing out of her butt, followed by a few bubbles and then one, two, three rocks!

The last one was the largest and she shook all over as it came out. Then she let go of the ramp and settled on top of the pipe, looking exhausted. Now the tank had this greenish looking cloud, so I called work and told them I'd be a little late, I had to change out the water. I didn't see her pass the first rock, but I'm guessing it probably went the same way and this "cloud" (I can't even call it diarrhea, it was pure liquid) overwhelmed the filters, driving up the ammonia and then the nitrate levels. I checked her over and the cloaca looked OK, no signs of blood or even swelling, so far so good.
I hope this is the last of the rocks, I don't think I (or Beaker) can take much more of this. I'll post some pics tomorrow.......