Alright - I'll give it a shot for what I know.
Front derailleur, they have the same type front derailleur, the 31.8 is the size of the seat tube on the bike that it's connected to. 31.8 is bigger than 28.6, so it's got a bigger tube. No real difference in that.
front & rear hub - 36holes vs 32 holes is the number of spokes. 36 holes is 36 spokes - which means it'll be a fairly bombproof wheel - it will be 4 spokes heavier than the 32 spoke wheel. If you're a very heavy or big person, you may want the 36 spoke wheel. If not, 32 spokes is probably plenty.
Stem... If you have a fixed stem and you want to change the length or height of your handlebars, you have to buy a whole new stem to do that... the bike shop may be willing to swap that out for you to one that fits you when they sell you the bike and not charge you for a new stem. Adjustable stem, you undo a screw and change the angle to raise or lower the handlebars. Adjustable stems are heavier.
I dunno about the difference in bottom brackets, but you can check sheldon brown's website.



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