Alright, may the heavens have mercy and this not jinx myself, but it appears all is finally sorted. I have drove the car several hundred miles, and for several days without any problems. These last few problems were cleared up by a bad PCV system and pre-cat O2 sensor (the one at the top). The car drives like an entirely different beast, and all is well. In the end, I have managed to do all of this work myself, without spending much on this car (purchase price plus all the parts and taxes). All in all, I have spent less than have than what the cheapest clubman in my area was selling for, and about a third of what I planned to spend to get one without high mileage.

Here is what was wrong and what fixed each problem
Hopefully this will help someone else...

In the beginning, the car was a formless void, and darkness covered the face of the deep in the form of all of these codes:
P0015 (camshaft position- timing over retarded)
P2187 (system too lean at idle)
P2178 (system too rich off idle)
P0137 (O2 sensor circuit low voltage (sensor 2))
P2096 (Post catalyst fuel system too lean)
P0301 (Cylinder 1 misfire)
P0420 (Catalyst System Below Threshold)

The car was driving at about 50% of where it is now with all of these codes

Fix for P0301 (cylinder 1 misfire): The coil pack was actually bad, I replaced all four coil packs with brand new Bosch units. I was fortunate to have some BMW coils around, which helped me diagnose the issue. The bad coil pack had orange (rust looking) residue were it pops on the spark plug.
the new coil pack increased drive quality to about 80%

Fix for P0137(O2 sensor circuit low, sensor 2) and P2096 (Post catalyst fuel system too lean) : New lower O2 sensor.
Drive quality stayed at about 80%, but the codes went away on their own will

Fix for P0015 (camshaft position- timing over retarded): One of the two VANOS variable timing solenoids was bad, so I replaced them both. The bad one was on the intake side, and its O-ring was worn out. It actually was making a hissing sound and leaking a very small amount of oil. Also, the one on the front looked as if it had already been replaced, due to the fact it had a different design than the back one. I replaced them both with new BOSCH units.
Drive quality increased to about 90% after the new VANOS solenoids, and the P0015 code did not manifest further.

Fix for codes P2187 (system too lean at idle) & P2178 (system too rich off idle): These codes may have been more related, or more unrelated than I am aware of. When I purchased the car, both were confirmed with my OBD2 reader, however, after I cleared the codes initially, they never were present at the same time. The car did show to be rich most of the time, and the code for running lean was much less frequent.
To fix this, I hunted for days. Ultimately I found my throttle body was covered in oil and the PCV hose was pumping a large amount of oil straight into the intake. I replaced the entire PCV system, which meant a new valve cover (PCV is built into the valve cover on the N12 engine) and hose. The hose may have been an arbitrary replacement, but nonetheless, it is done. I realize the PCV should make a car run lean, but for some reason it was making this one run rich. The throttle body had oil and sludge on it, and there was sludge around the edges of it, possible affecting airflow.
New PCV system (valve cover and hose) increased drive quality to about 93%, and the car ceased to run rich, and changed over to lean (according to the check engine lights)

P0420 (Catalyst System Below Threshold): The upper O2 sensor fixed this, and made a huge difference in drive quality. Drive quality went up to where it to where it is now (100%), and the code P0420 went away.

I made a tool for removing the top O2 sensor, and it made this task extremely easy (see picture, it is a long 22mm 6-point socket with a slit cut, and welded to another socket. With this tool, the old sensor came out with ease. All I had to remove was the bracket holding the wires. Didn't even have to put the car on ramps, it was a 10 minute or less swap out. check out the bad O2 sensor.

 

Congrats, great re-cap! Well done!

 

Clogged cat?

A user named MINIPWR has a 12 page thread that was the result of a clogged cat.

 

I hope not, and I doubt it as well, as the car is running great after everything detailed has been performed on it.

 

Incorrect. Higher octane is actually a slower burn - more controlled, as well.

You'd be better off with 93 in ANY MINI engine, whether it's turbocharged or not.

 

Running rich will kill a cat. And a blocked cat will show issues when pulling hard and or high rpm.

 

You can buy O2 sensor sockets for a few bucks. And I'm 90% sure all O2 sensors are SAE, not metric, even in our cars.