The test procedure I recommend is based on using a spotmeter to measure the reflectance of a white card on the baseboard, in which case the "target" value is EV 4.0 for 100- speed film (EV 2.0 for 400-speed). When you've arrived at that setting -- using one of the film/dev combinations I mentioned as representing an honest ISO 100 rating -- run the test through the Plotter and let it find the "ISO" point for you.
Ideally, it should identify 2.4 as the ISO speed point but you can use any value it finds; you're simply creating your own standard here; there's no "right" value, just a recommended one (2.4 is a nice even number that places the curve family in the graph space at a useful location). Once you've identified that personal speed point, consider it to represent the real ISO speed, and use it as a reference for calibrating all future film tests. If you enter this personal value into the Plotter (Option window) and activate it, the Plotter will automatically calibrate all your test film charts to reveal each film's real EFS values.
I don't know what reading you should get with an incident meter (cone on or off) but you can find the proper value experimentally. Do the 3-film test I suggested, let the Plotter find the speed point, then calculate the exposure adjustment necessary to shift the speed point to 2.4. Whatever test settings are required to do that can become your standard settings for all future tests. If you use an incident meter for this setup, using it with the cone removed (or replaced with a flat diffuser) is probably best; you're not interested in the 180° coverage of the normal dome.