#2
There's really no reason for it other than when pedals were new-ish and most guitarists just used one pedal at a time, there wasn't any standard for the in/out layout. Some ended up being left-right, some right-left. I think the standardization probably started with the fact that you have to unplug the input to save the battery when you're not playing, and most people are right-handed, so it makes a bit more sense to put the input on the right side.

That said, it's just a guess and I really have no idea.
#3
well you read from left to right... a lot of amps inputs are on the left. why not have your pedals go from left to right?

that's my guess, although i've been laughed at a number of times for saying that.