To recap:
The diamonds you've already cut are 3.5" unfinished.
And you need diamonds that are 3" unfinished.
Is that right?
Why can't you just cut them down to the size you want?
Are the diamonds sewn to each other, or are they made into a rectangle, where do the squares you mentioned go, how are the diamonds finished in the pattern, what is the height of the diamonds?
Do you have a picture you could post of the pattern, or a link to it somewhere online?