Remember, nobody is going to go back and measure which blocks are the original size and which are not. As long as your seams are consistent and you shave a consistent amount off, then you should be able to align the blocks and make the seams match. If you have too much difference, then your seams are not consistent and you may want to go back to the beginnings and figure out where the seams get off in the first place.
I just had to deal with that topic when my HSTs came out a little wonky and I had to fudge my whirly-gigs.