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You need to check the diagrams again.

The XL16i requires 80% airflow for first stage.
If you connect Y1 to Ylo in the furnace, with no power to BK, you only get 80% of 50%. That is only 40%...

Yes

To have Comfort-R in the heat mode of the heat pump, the wires for O from the thermostat and O to the outdoor unit need to be disconnected from the furnace control board and connected together...

Why would I want to do that? On a Trane XL16i or AS Heritage 16 system , the control wires for 1st stage cooling connect to Y2 on the furnace control board or air handler LVTB. ;)

If O from the outdoor unit and the thermostat are connected to O on the furnace control board, no jumper should be between the 2, or your heat pump will be stuck in the cooling mode.

Ideally, O...

which model do you have?
If it is the Heritage16, then yes, the w14 jumper would need to be cut.
y1 from the thermostat and outdoor unit would also need to be run to Y2 in the furnace, and Y2 from...

Nope, its on or its off, thats it.
It will ramp up some to maintain airflow as the condensor coil gets dirty.

The fan doesn't change speeds on the XL16i when it changes between 1st and 2nd stage. The control voltage to signal the ECM module on the motor to turn on is from the 1st stage call. Y2 to the...

I wouldn't say it makes "no noise". You can just barely hear the solenoid pull in, and a very subtle change of tone from the compressor if you listen closely.

The W14 jumper definatly needs to be cut, and the dip switches correctly set for a 4 ton system.

Since it seems you are looking at this yourself, how is the control wiring connected?
The wire...

There should be a 20% difference in airflow through the indoor unit between 1st and 2nd stage.

I have installed and serviced quite a few XL16i systems, but couldn't walk up to one and tell you...