I bought a set yesterday and they seem odd. The original tuners i took off (Fender USA 2009 Strat) are numbered 1-6 in roman numerals. I assume this is to stagger the post height. The locking ones from guitar center are numbered in Roman, but I have one #4, three #2's and two #3's. Is this correct? I think I got a bad of leftovers maybe?

no thats the way they are, I don't think there is any significance to the numbers just make sure when you install then you get the stagger correct. I have a set and they are that way

Right I think there are three heights, shortest 2 go on on the low e and b and tallest 2 go on high e and a middle two go in the middle

There's 3 heights. The tallest 2 are for the E & A strings. The middle 2 are for the D & G strings. The shortest 2 are for the B & E strings. This will allow you to remove the string trees.