my replacement tone and Vol pots were larger then the originals, so as long as they fit who cares. its not like your trying to make it all original.
as for the intonation, your tuner isnt really telling you what string as much as its telling you what note it is. Id assume its somthing like my qwik tune in function. with a simple set of red/green lights.
Id suggest get a better tuner, like a Korg CA-30 or similar.
let me also say this, when I adjust for intonation, I use open and the 12th fret, and again if its a 24 fret neck. I was told to assume that some of the frets wont be perfect, so as far as the 18th being the correct note I done know.
as far as the lefty thing goes, I dont see it being a large issue. Ive seen/played a few like that and never heard of it being a problem..