Ok, ill try to help.
12mmx1.25 is simply the thread size of the threaded insert inside the ****. So when you order you MGW you choose between 12x1.25 or 1.75. You would get the **** to match the threads of the shifter you ordered. 12x1.25 is the oem size for our cars so i would go with that simply because it makes it easy ot order another shift **** down the road its just the same as any regular mustang shifter.
I cant help you with the 401A shift boot adapter as i have just the regular boot/adapter.
as for **** size, do you have big hands? yes? go for the bigger one. the ***** that CJpony parts sell are 2 1/8" so they are right in between so either way should be fine. or just get the smaller one so save the $5.
Hope that helps.
2013 Mustang GT/CS: Borla S type axleback, Various LED lighting, CDC hood struts