Very pretty! I would embroider the flowers after fulling - even if you're just fulling a little, the wool could shrink enough to pull the embroidery in more than you want.
Maybe do test swatches of embroidery before fulling, and embroidery on the fulled swatch to make sure you're getting effect you want.
Embroider after fulling. I'd actually recommend using crewel wool rather than cotton, but I'm obsessed with crewel. Embroidering on knitting with any drape is kind of a pain, but me prepared for it to be a tiny bit uncomfortable to embroider on the fulled garment. You may want to bring out the thimbles.