I do alot of hand piecing and I have added an extra step to my stitiching just for this same issue. What I do is I cut my pieces out per directions, then I go to "my" next step.
I draw a stitch line by measuring an 1/4" from the cut edge using a nice sharp white crayola pencil (for dark colors) or mechanial (?) pencil (for the light fabrics) on each side of each piece. And since I've started doing this things line up for me regardless if it's a big block or a 2" square for my doll/mini quilts.
I also always use the same ruler and needles for the whole project. Since then I started that, all my seams match up so I have less frustration and found it so worth the extra step.
Hope you might consider adding this in your hand quilting project.
Tricia