Ok here's the story
2010 manual transmission, 186K, well maintained.
Sudden onset while under hard accel of inability to shift into all gears, clutch slip, and clutch pedal throw slightly shorter and softer.
With double clutching, persistence, and unkind swear words was able to motivate gear shifts to make it home.

Findings:
slave cylinder with torn boot, clutch fork felt loose to the hand. Replaced with slave, dropped the trans. Release bearing found to have some play and dragging on rotation, "fit" didn't seem appropriately snug with the fork, pivot bolt in good condition. Manual rotation of the main shaft produced the noises in the included video.
Pressure plate with 2 of the springs bent inward 3-5 mm. Friction disc at 4 mm, all the springs were sloppy loose and 3 of them had an area of grinding marks on the spring. Flywheel looked fine. Pilot bearing slightly difficult to turn without obvious wear.

Purchased an eBay clutch kit - XTR Stage 2 with chromoly lightweight flywheel, $209 shipping included, included throw out bearing and pilot. Slightly leery about using the bearings (given EBAY origin story) but actually appeared high quality and money and time constraints meant it needed to be finished.
Replaced clutch without issues.
Elected to not dive into gearbox and differential, again time and money.
Initially drove without issues.
2nd day of driving went into limp mode. Scanner reads P0300 and friends. All cylinders with random misfires. Engine seems to be running normal. No discernible misfires. Scanner counts show roughly even numbers of misfires in all 4 cylinders. Cleared it out but it comes back; generally at hwy speed. O2 sensor data normal. Long and short term fuel trim seems high 10% and 16%. Timing is advanced up to 36 depending on driving condition. Pulled MAF, MAP both normal appearing, cleaned with appropriate cleaner. Cleaned throttle body, Cleaned EGR - seemed to have a decent amount of carbon on it. I am getting EGR error up to 100% but when engine warms it normalizes out and the misfires happens independent of EGR error. AFR commanded and measured are roughly equal but occasionally out of sink, previously had never witnessed them out of sink (I generally drive with live data being displayed on my car screen). I performed a crankshaft position sensor relearn procedure and repeated the idle learn procedure. Next steps I plan are to pull and inspect plugs and coils and perform valve adjustment. -- I will update when this occurs.

New issue. Today noticed whine or whirring sound (similar to the straight cut gear sound when you drive in reverse). It occurs only with the car in gear, generally at lower rpm + under loader or engine breaking. Push the clutch or let off the gas it goes away immediately. Leave it in gear and let the engine slow the car and it continues. There is also a very slight vibration palpable in the gear stick. Revving the car does not produce the noise with the clutch in or out. Refer to the included video- I am concerned noise is related to bearing within transmission perhaps input shaft or pinion bearing in the differential.

For some time I have had a cyclic vibration over 65 mph. One second on and one second off. Once it begins it gets worse with increasing speed and is moderately hard like things in the car also shake. I had chalked it up to wheel balance as one of the tire got a dose of fix a flat but given these new issues I wonder if its not related...

I have previously replaced front wheel bearings and CV axles.

Any advice on how to narrow the noise down? I will likely just replace the entire trans with a low milage unit. But if I knew for sure was X and X wasn't too bad I might just fix it.

Any advice on other steps to solve my misfire? It seems weird it happened after the replaced clutch and flywheel. If crankshaft position sensor was bad should it throw other codes as well?

Dumb question - Will manually rotating an engine in both directions affect the timing or valve clearances in anyway? I did this when removing the flywheel to keep it stable against wrench torque.

 

I've had misfires for two different reasons.

First was when I ran out of fuel pressure maintaining high RPM for more than 6 or so seconds, with a supercharger. I replaced the factory fuel pump with a Deutschwerks DW65c. I'm not saying you should replace the fuel pump with the same one, or even that the fuel pump is necessarily bad. But could be something is interfering with the engines ability to get enough fuel. Whether its a bad pump, damage to the line, etc.

The second was when my spark plug threads got damaged and the plugs themselves came loose. Replacing or even just retightening would clear it for a while until it came loose again. Only fix was to rethread the port.

That said, there's a major difference between the two. In the first case, it involved ALL cylinders (P0300). The second was limited to cylinder #2 and later #4. This cropped up two different times, so really 3 sets of misfires... though, I may be experiencing it again with the remaining ports I haven't rethreaded. I'll be rethreading them as part of my upcoming repair project.

 

I cant answer a single question you asked 😂 More information than i'm used to. But you said you installed a lightened flywheel and ive seen threads stating that our car does not like those. Something something knock sensor, something something f*ck.
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I didnt like the stock clutch.. too aggressive. Exedy's has a smaller friction surface. too much friction makes for jarring clutch engagement. add in some clutch dumps and stalls, can smash those springs (or so's my theory based on finding my own being smashed)

I'll have to re-read yer post, but it sounded like a lot of anomalous stuff, not inherent to the vehicle. and like you know your stuff. So my first thought is overly light flywheel, maybe imbalance