Thread definitely affects size of blocks. For me, it also affects accuracy. Thinner thread such as Aurifil 50/2 works much better for me than more traditional 50/3 ply thread.
I use strips of adhesive moleskin on the bed of my machine to provide a physical guide for me seam allowance. I use my favorite ruler with fine lines, place it under the pressed foot, lower the needle until it touches just to the right of the 1/4" line, lower the pressed foot to hold the ruler in place, and check that the ruler is running straight from front to back. I cut strips of moleskin with my rotary cutter and a ruler, peel off the backing on a strip, then butt he moleskin up against the ruler to position. I usually place another strip of moleskin on top.
Sew three 2.5" strips together, iron, and they should measure 6.5" across the width.