Rough Engine Idle in Neutral

Hello! Long time FF reader, first time poster. I need some troubleshooting help from you guys.

I have a 2005 Focus ZX3 2.0L Duratec manual 5-speed with about 130k miles. My dad bought it new and we did a decent amount of mods in 2007-2008 (listed at the bottom), I have owned and daily driven it for about 3 years now. My issue is that the the car runs rough at idle. Before you say it's an EVAP/vacuum issue, please continue reading, bc this is weird.

I think it's an issue with the ECM getting o2 sensor readings when I am in neutral aka not in gear.

Here's my troubleshooting and pertinent information:
The two codes I've had are P0171 and P2195. P0171 has been the predominant code, but the past few weeks have only been P2195.
I believe this issue has been noticeable to me for maybe 1-2 years now.
I had my clutch replaced within that 1-2 year timespan (not saying that is related).
For most of this time, I've thought it was likely an evap or fuel delivery issue. In the last 3 months I've cleaned my intake filter, replaced the fuel filter, fuel pump, MAF sensor and b1s1 o2 sensor.
I've propane tested the whole engine bay trying to find a leak and could not find any change in RPM besides just at the intake to make sure propane was actually coming out lol.
I begrudgingly assumed it must just be the PCV valve or hose as I've seen a lot of other MK1 owners have cracks in those.

So here's where my thoughts changed. One of the reasons I changed the o2 sensor was my OBD scanner showed that b1s1 o2 sensor was pegged solid at 0.0v when I was not moving and at idle. In turn, the STFT would MAX OUT at ~66% trying to add as much fuel as it can and my engine would not have a good time. So probably a big vacuum leak, but maybe the o2 sensor is bad. So I replaced the o2 sensor with a new one let the ECM relearn itself for 5 minutes and took it on a drive and same issue. I parked in the AutoZone parking lot disappointed watching my o2 sensor give 0.0v while not moving. Then I put it in 1st gear to turn the car off and BOOM the o2 sensor reading maxes out to .935V and the STFT starts bringing itself down to normal. I put the car back in neutral and o2 goes straight back to 0.0v and STFT starts going up again..

This is 100% repeatable. When I take the shifter out of gear, no relation to clutch pedal position, the o2 sensor goes to 0.0v. When I put the shifter into any gear, the o2 sensor starts reading accurately again and the fuel delivery goes back to normal and the engine runs great.

I tested this on my way home from work today by sitting at every stop light in 1st gear with the clutch down and I had zero issues and my o2 sensor reading and fuel trim readings were 100% normal.

So - what the heck is happening? The car is tuned with a 2008 era SCT tune that hasn't been changed since we tuned it back then. Can the tune go bad? I have the Steeda short throw shifter installed, again it was installed in the 2000s. And my clutch was replaced in the last year.

I know there is a reverse sensor in the shift tower that tells the reverse lights to come on. Does the car know what gear I'm in and if I'm in neutral? If so, it seems like it just doesn't read the o2 sensor data when it's in neutral.

Forgot to mention - the car is not going into open loop, it is still in closed loop when this is happening hense the STFT adjusting to crazy numbers when the o2 sensor reads 0.0v. When the car is warming up I have data logged it running in open loop and it runs just fine in neutral until it's warm and enters a closed loop.

I have pictures of my data stream, and I also downloaded LiveLink 6 to data log a drive using my og xcalibrator2 lol, so I have an excel sheet from that as well. I can post a few pictures shortly.

Modifications:
Steeda cold air instake
Magnaflow exhaust
Steeda short throw shifter
Focus Central style 67mm throttle body
SCT performance tune from 07'-08'
replaced thermostat, b1s1 o2 sensor, fuel filter, fuel pump, MAF sensor
Eibach Suspension
other non-related to this issues upgrades