I don't think the stuffing you use will be the determining factor in the ultimate size of an article....I use polyester fiber fill, too, and like it a lot...and, don't find it lumpy if I'm careful to fill it evenly. For myself, I know that I knit loosely and thus my garments/articles tend to be bigger that the instructions say they'll be...so, I always knit with smaller sized needles. In your case your article would have been smaller if you'd used just a single piece of yarn.

I agree with Sandra. If you used wool yarn, you could try felting the mouse form before stuffing. That would help prevent stretching.

Annie