Outline of the problems on the 06 EX Coupe 5 speed, roughly 115k miles on the clock:
Please note, I am a nissan person, and am used to insanely stupid cars for their insanely stupid owners, and modern honda land... is not that. I am very out of my element.

Complaints about a slightly "rougher" than usual idle the last few days. It needs the lower torque arm/mount replaced, we just have not gotten around to it. I assumed it was this and ignored it.
A too Lean CEL History, but its never current when I check. Sometimes Id get the call the light was on, and by the time she got home it would have magically gone out.

After 2 days of this the car can no longer keep an idle. It will cold start rev right to about 1400 and then "notch" down about 200 RPM at a time until around 500 and lump around before eventually stalling. Cold or hot does not impact the lumpy idle, and it sounds like its misfiring randomly but there is no fuel smell out the tailpipe or any visible smoke. When its bouncing around the Lightest touch of the throttle will instant kill the motor. no CEL or codes. It feels like about 30% of the pedal travel is needed to get the car to 2000 RPM in neutral and everything below that just kills the motor, unless you then floor it.

If you can keep the RPM above about 2000 its smooth, and runs fine without any real hiccup or issue, however as soon as you drop this threshold it will probably cut off, or instant drop to around 500. If you take your foot off the gas it will stall coming to a stop. No Cel or codes. If you dont rush it through gears, it will actually stall on you mid change if you are driving like grandma or you are used to double clutching because your 30 year old crap box lost its syncro's months ago.

Things we have so far looked at

• Checked under oil cap to make sure the block did not crack /mix coolant and oil. All Seems well. the Vin is outside the block casting defect range anyway.
• PCV seemed to be stuck, replaced valve. Marginally helped the idle bouncing reducing severity and increasing run time without user intervention. The engine does seem to have a little more pressure out the oil cap than I am use to, but the oil stays clean and looks almost new when we change it, suggesting its not a lot of blow by.
• The Air flow meter was reading wild swings in flow, and we replaced that just to rule out the sensor. No change to speak of. Same wild readings.
• The second you pull any spark coil lead, the idle gets worse and the car cuts off, with Appropriate CEL is triggered.
• I cleared all the codes, tried my best to get the car through the idle relearn procedures but it did not seem to resolve anything.
• Inspected for vac leaks. I swear I can hear one but maybe its just a normal honda intake sound. We basically coated the entire intake side of the engine with carb cleaner just trying to find any leak... idle never sped up.
• Checked Primary O2, voltages read out more or less fine, pulled it and looked at the probe end and there are no ashy deposits I'd expect if it really was running lean. No black soot, not wet with oil or fuel.
• No lifter tap, so I assume the lash is set accordingly. If it were out far enough to cause it to not run, ID imagine they would sound like a rock tumbler, or like my nissan.
• Checked to see if low fuel pressure by trying to crimp the inlet soft line to the rail, Couldn't close it off by hand, but did not get a actual gauge on there yet.\
• battery at 12.55v when the car is set to on, but not running. Its 14.4v when running.
• Coolant temp sensors are New as of last year, and Honda OEM from the dealer ( and boy are they proud of those suckers, and their brand coolant too)

Odd Readings from Live OBD2:

• Closed throttle reads out at 18%, WOT reads out at 78.5%. This seems odd to me, like closed should be 0-5, and WOT should be 100... But I dont know if this is a scan tool issue, or a real issue with the TPS, or just honda being honda?
• Fuel Circuit 1 seems to be in closed loop when cold, and when hot. I assumed this would change, but anywhere from coolant temp of 80 to 205 always read out as CL
• ERG seems to work, but occasionally would report error values of 3-5% in Live Data. But this might just be it having to be slammed open and shut to keep the car running.
• Timing is all over, but I cant tell if that's a cause or symptom . anywhere from 5ATDC to 25BTDC and basically never constant.

Untested Ideas:

• Failing Crank angle sensor? Though I'd assume this would prevent it from even firing.
• failing throttle body actuator/ Idle Air Injection valve?

I would just take it to the dealer but we are very tight on funds right now, and honestly probably cannot even afford the dealers shop times. Our honda dealer charges insane prices for everything.

 

Solved:

there is a 10mm hex head bolt somewhere around the number 4 intake runner after the throttle body that threads in almost perfectly horizontal from the firewall side, towards the front of the car.
Its roughly halfway down the head on the intake/backside...I dont know the thread pitch or diameter, but had one to replace it with.

It had fallen out, leaving a giant open vac leak I could hear, but never see, never hit with any sort of spray or carb cleaner etc. I could not get a photo of it with a phone for posterity in case anyone else had a magic leak.
Could only feel around blindly until I covered up the leak with a finger.

I guess this port is used for a vac source on the automatic version of the car, and just plugged with a bolt on the 5speed.
Used a air box hold down bolt from our EF hatch to plug the hole, and relearned the idle, car is back to happy as a clam with O2 lambda sitting between .995 and 1.007 now under cruise and normal driving in gear, with steady state often sitting perfectly on 1.00.

I had removed most every vac line today trying to inspect them all for leaks, got fed up, put it back together and was ready to call a tow. Looked one more time for the leak and thankfully found it.