I just finished making a D9P quilt top that for a variety of reasons HAD to come out to 9.5" when finished. If I were to have used all 3.5" squares, it would have ended up smaller because some of the blocks are cut, turned and sewn back together. I am going to attempt to translate what I did into measurements that will come out to 12.5". Hopefully, this makes sense.
Your blocks will line up as:
1 2 3
4 5 6
7 8 9
Blocks 1, 3, 7, and 9 should be 4.5" by 4.5".
Blocks 2 and 8 should be 4.5" by 5". You would sew them together, matching up the 4.5" side of block 2 with the 4.5" side of blocks 1 and 3 (same thing for blocks 7, 8, and 9).
Blocks 4 and 6 should also be 4.5" by 5", with block 5 being 5" by 5". Again, you would want to line up the 5" of blocks 4 and 6 with the 5" of block 5.
You would end up with three strips. The top and bottom rows would be 4.5" wide by 13" long. The middle row would be 5" wide by 13" long.
Then sew the three strips together. Remember, when you cut the D9P, blocks 2, 4, 6, and 8 get cut once through. Block 5 gets cut twice. So when you sew them back together, you end up taking up the extra space in the seam allowance. This should give you a 12.5" square block.
I know that I am not doing a great job of explaining this, so hopefully someone else can do a better job of it.