Hi, 
I have CNCv3 on Wemos D1 R32 board, and I have it perfectly working with LV8729, but unfortunately when I plug in S109 it does not work for some reason, it is not able to boot, I get this error when debugging verbose: 

I'm guessing the GPIO12 pin, used for all four drivers ENable, is being pulled logic HIGH by S109's when it must be LOW.

Install a pulldown resistor if you'd like to test that theory, perhaps 4.7k or 2.2k to be sure it's LOW at boot.

The 2208/09, S109 and LV8729 have a different pin arrangements. So if you cable for the LV8729 which has the Pololu pattern is It going to work for the A109? Yes, the is the same, but the coils are reversed as will be the direction rotation. The S109 can put out 4A a 0.9A motor will not take that for long. The LV8729 cable is also fine on the 2208/09 driver, but again the coils are reversed.

Well I forgot to mention when i short EN and GND i get TMC2209 working, but S109 does not and shows same error,  I will try with resistor, unfortunately I do not have one at hand with those specifications so I have to order, or scrap something :D  

Thanks George, I newer saw that, I am still prototyping so I do not have direction at this moment but it could make me confused indeed. 

Do not worry about current I take care I do not overload my steppers, I even keep them under their required amps(~70%), and it works flawlessly as they are not under big load, no need to waste electricity :D