Hi Bob, Welcome to Yamaha Synth and thanks for the question.

Here is your checklist:
The Organ Voice is assigned to the LAYER PART
Press [EDIT]
Select 02: PART > [ENTER]
Use the Cursor UP/DOWN to navigate to PART EDIT 03: "EFFECT-A" > [ENTER]
Make sure you are set to edit the LAYER PART, you can do so by holding the [PART SELECT] button and touch the [LAYER] button; the Part being edited will be listed on the left side of the screen... "Edit Part LAYER"

Assign the "Rotary" Speaker Effect from the T&R (Tremolo & Rotary) category to the LAYER PART as EFF A
Cursor DOWN to view the Rotary effect's parameters
Take note of the current initial "SpdCtrl" (Speed Control) setting "slow" or "fast", because if it is "slow" you will later set the MW = "EFF(+)" to switch to "fast"; if the initial speed is "fast" you will need to set the MW= "EFF(-)" to switch to "slow". The initial Speed Control setting determines the speed at the time the program is recalled (MW = 0) down position

Press [EXIT] once to return to the EDIT PART screen
Select 05: CONTROLLER > [ENTER]
Set the "MW" according to your initial Speed Control setting. "EffA(+)" for slow-to-fast; "EffA(-)" for fast-to-slow

Sounds like you have done this, now let's check the other parameters that can affect the outcome:
Press [EXIT] once to return to the EDIT PART: LAYER screen
Select 06: RECEIVE SWITCH > [ENTER]
Here make sure your Layer Part can receive the message it needs to flip the speed switch (cc001)
Make sure both "CC" and "MW" are set to ON _ use the UP/DOWN cursors to view the various controller options...
"CC" Control Change must be ON for this Part to respond to any controller messages
"MW" Modulation Wheel must be ON for this Part to respond specifically to the mod wheel.

And as you noted, make sure the PART EFFECT [A] button is lit when the LAYER PART is selected for Edit

As you move the MW to the up position the Rotary Speaker switch will transition from one speed to the other at the Transition Time as programmed within the Effect's parameters. You have separate Transition Times for the high frequency Horn, and the low frequency Rotor. In general, in a Leslie, the Horn transitions faster than the large Rotor just due to the mass (size and weight) of the rotor drum - this is customizable within the Effect. You can make the "belts" as tight or loose as you desire.
"S-FtmRt" = Slow to Fast time Rotor
"S-FtmHr" = Slow to Fast time Horn

Press [STORE] to write your settings to a Performance location.

Let us know.

All those settings were as you indicated, but the rotary effect was still not working.

I found the problem. The Effect On-Off switch was Off (Part Edit: 01: Play Mode: EffA/BSw). When I changed it to ON, the effect worked.

Initially when I tried to change that from OFF to ON by turning the Data Wheel, nothing happened. I checked the Reference Manual and found that this can only be turned ON for two parts. It was already enabled for the Main and Split; since I'm not using the Split, I disabled it there, and was then able to turn it on for the Layer.

Thanks for the walk through. I wasn't aware of the (+) and (-) variables of the effect controls.

Bob