The intent is that you should replace all of the flap sections in the original config file in their entirety only with the lines in my readme file.

Sorry about that, looking at your question I can see there is some ambiguity there.  So when you are done the only lines you should have in your config file with respect to the flaps are:

[flaps.0]
type= 1
span-outboard= 0.632
extending-time= 40.0
system_type= 1
damaging-speed= 250.0
blowout-speed= 300.0
lift_scalar= 1.000
drag_scalar= 1.000
pitch_scalar= 1.000
flaps-position.0=  0
flaps-position.1=  2
flaps-position.2=  5
flaps-position.3= 15
flaps-position.4= 25
flaps-position.5= 30
flaps-position.6= 40

[flaps.1]
type= 2
span-outboard= 0.327
extending-time= 10.0
system_type= 1
damaging-speed= 250.0
blowout-speed= 300.0
lift_scalar= 1.000
drag_scalar= 1.000
pitch_scalar= 1.000
flaps-position.0=  0
flaps-position.1=  1

[flaps.2]
type= 2
span-outboard= 0.589
extending-time= 10.0
system_type= 1
damaging-speed= 250.0
blowout-speed= 300.0
lift_scalar= 1.000
drag_scalar= 1.000
pitch_scalar= 1.000
flaps-position.0= 0
flaps-position.1= 0
flaps-position.2= 1


This produces the desired result in terms of the flight model, but unfortunately the flight model will  no longer be synchronized with the flap animation of the physical model -- all leading edge devices will now extend with the first notch of flap application.  I have found a way to correct this and will eventually post an update. I will also clarify the instructions in the download readme before then.