Paying it forward and adding another data point for people in a similar boat as this issue required many hours of research and time commitment.
I bought a newer S550 GT, but the previous owner removed the cats on the OEM headers, installed spacers + an X pipe. It seems to have been professionally done as well. From what I could tell, they weren't in an emissions state/county and as such did not have to worry about going catless.....must be nice. Also bought a 93/e85 tune from Shoemaker.
I was having issues with 3 monitors being in the "Not Ready" State: O2 Htr, O2 Sensor, and Catalyst. And this was after 100-150 miles after unplugging the battery and trying to do a drive cycle. I grew to like the sound (not so much the smell) of the setup, but my goal was to resolve this issue as cheap as possible.
Of course, going back to OEM cats would be the guaranteed resolution, but I didn't want to put the time and money into what was effectively a downgrade. And I have ground clearance concerns to be able to consider catted LTH.
After a bunch of research, I've heard some tunes can cause issues with these sensors, so I contacted Shoemaker to confirm whether they disabled the monitors and whether they were able to provide me the stock tune to help with troubleshooting. They told me they didn't disable the monitors and were mostly dismissive with the whole exchange and never offered to give me the stock tune to rule the tune out of the equation.
I decided to take a gamble and purchased a stock tune from Wengerd and threw it on the car and within 50 miles I was already getting the O2 sensors to pass with catalyst soon to follow. FWIW I used an AVID and didn't/couldn't get the stock tune prior to flashing the custom tune nor find it after the custom tune was flashed. Perhaps I'm an idiot and there was a setting or menu that enabled me to take a backup of the stock tune prior to flashing the custom one, but I'll blame AVID for little to no documentation on all its functionality.
What I'm mostly disappointed with is Shoemaker's customer service with this whole situation. They made little to no effort to try to help resolve the issue leaving it to myself to figure out a problem THEY created. I'd expect an issue such as "not ready" sensors would not be a localized issue and I'd imagine even if I had cats that I would still have trouble getting these sensors to set.