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Ok no need to be confused buddy it's nothing special or difficult to get your head around. I'll explain for the sake of others thou it's all on the forum somewhere else.!

You have G540 which is...

You bring up a good point. Depending on your Windows settings you may or may no see the .exe extension on the file.

The DOS box or command window is supposed to come up like that.

Scorch

Yep go to ports & pins-Motor outputs and change Dir lowactive. So if ticked un-tick or vise versa.

I got the following from Arc Euro Trade and it fitted my CNC3040 letting me use 1/4 shank router bits.

ER11 Collet Nut - 050-110-11530 - £6.95
ER11 Collet 1/4" - 050-110-11240 - £6.00
...

If may ask some really basic questions, is there a basic setup guide for Mach3 with the CNC 3040 with YooCNC controller anywhere that anyone could point me to?

Yes you can download the machine...