I would work towards making the three sections the same size, you're almost there now. I would then run a strip of fabric lengthwise between the sections. Maybe you look at that as cheating but sometimes getting done is better than perfect. You could add nice wide outside borders to match the inner strips and call it done. What you have done is very pretty!

matching seams
 

I too become frustrated when the corners are off. This is what I do after sewing the piece seam; I keep a small Dritz black ruler next to my machine. It has a moveable red marker on it. I move the to size needed. If the seam is off, then I sew it again. then I move on to careful joining...looking down the seam to make sure the length of the seam if lined up beyond the end (because you sew 1/4" below the edge).

Sometimes it's best to just alter the pattern. I've made several postage stamp quilts, tablecloths, etc. I found by alternating the seams from row to row, there's a whole lot of stress alleviated. Simply have the seams from one row fall in the middle of the square from the previous row. Makes life so much simpler and I must say that the look is, if anything, even more "postage stamp" looking.

Be kind to yourself. Enjoy your journey.

Check your seam allowance for evenness. I bet that the amount of the seam allowance varies. If so, that is your problem for having trouble making things match. Be accurate when you cut and stitch to get really accurate finished patches. Also, when hand piecing, don't stitch into the seam allowance and you'll have more "play room" to manipulate the seams to meet. Good luck--you chose a simple, but challenging size.
SandyQuilter

It looks great in the pictures. Remember others are going to look at the overall affect, not individual corners of the tiny pieces.

When hand stitching, using a 1/4" seam allowance (or whatever you are using)...keep it accurate. Don't stitch to the very end of the squares...stop the width of the seam allowance from the edge (1/4", or whatever the seam allowance is).

When joining rows/sections...stitch to where the joined squares are, put the needle through the seam allowance, at the exact spot your stitching stopped (1/4" stop point), and bring it out the other side...you don't want to stitch down any seam allowance, as this will throw your seams off, no matter how many pins you use. If you have a seam that is off a stitch or two...try pressing the seam allowance in the opposite direction...sometimes that will help them line up. Has to do with the thickness of the thread or something.

Another important thing when hand or machine stitching...press every seam...press with right sides together (set the seam) then press them to one side or open, however you do them. Pressing will help with lining up the seams.

I'm amazed at your patience and tenacity. Best wishes on such a large task.