The way I change the size of a block is to begin with the FINISHED size of a component of the block, make it larger or smaller, then add the seam allowances back on. If the cut size of the center square is 3 and 1/2", then it's finished size is 3". You want a 6" finished size, so you cut the center square at 6 and 1/2".
The other two colors are cut at 3 and 7/8, which sounds to me like you'd be making HST's that should finish at 3". You should start with 6 and 7/8" squares, sew into HST's and see if that size works.