Chasing gremlins

If they’re the same at idle (value doesn’t matter) there’s probably no leak.

On the contrary. This is a myth. A stock bike idling should be in the 600s iirc. 900s is getting close to atmospheric pressure. 900s are pressures the MAP sees at wide open throttle I.e. lots of air rushing in. And so the ECU dumps in fuel to match and maintain AFR.
Trouble is when the bike is at or near idle, I.e. little air going in, and the MAP sensor sees 900s, the result is loads of fuel dumped in and causes mad rich condition causing the black smoke and bogging and dying the guy is seeing.

The MAP sensor seeing 900s is probably because the vac tube on it is loose or cracked or one of the rubber blanks on one of the other 4 nipples on the throttle bodies is missing or broken.

Besides the 970hPa MAP values the screenshot also showed the injector pulse time of 13ms which is long afaik so looooads of fuel being dumped in.
But that's the result of the 970hPa MAP value.
What's causing the MAP sensor to see 970hPa is the problem here. Its seeing almost atmospheric pressure.
 
At idle, the mixture is controlled by the stepper motor through the isc valve, no?

i will try to answer this
with the stepper motor retracted the throttle plates go to almost a closed position (if someone hasn't mucked it up) primary tps should be near .60 to .62
when the key is on the stepper motor comes out (should be near the .72 to.74 and gives you a measurement at the nut) if that is correct the ecu will vary the air/fuel ratio to achieve the idle desired (in my case 850 )
this is jut my opinion others may have a different one
 
Once the bike has warmed up the stepper motor is no longer in play, is my understanding. So, I think the vacuum leak and/or fuel filter is the most likely culprit. I've had both of these in the past cause these kinds of issues (along with a bad TPS). You've changed that and assuming it's not binding (or defective) we can rule that out.
 
So based on this analysis it's probably a combination of problems, starting with mainfold air pressure and injector pulse timing. The later can be address with a remap and reset of adaptations (probably), the first appears to be a mechanical problem, the sensors working fine (no code thrown) but the pressure reading is out of whack for idle conditions.
 
I hadn’t looked at his screen shots. So you’re suggesting that all of the map tubes are all leaking badly and seeing virtually no vacuum? Or maybe the sensor is broken. They’re certainly out of balance. In the earlier Roadsters, the F-L switch is at 31% throttle so it would be running really rich off the L tables when he is cruising at 60 mph, where he says it’s running fine.
 
Quick update. . . Lifted the tank and one vac hose was disconnected and the intake from under the seat was disconnected from the large plastic intake on the throttle bodies.

It was a pretty substantial improvement.

Still idling rough, but could just need a solid clean out (spirited riding)

Edit: stalled after three minutes of idling.
 

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Looks better! The throttle bodies are significantly out of balance. The differences should be no more than 10hPa.