I've only taken hormones for 6 days, then went off to store some of my sperm, but just yesterday my nipples began to hurt and now I feel a clear dull pain everytime I press them. Has this ever happened to anyone else?

Your results will depend on the method of delivery, but it'll take time for hormones to return close to "male" levels, and your body won't necessarily drop what it's doing the moment your hormones are back to their starting point.  A quick drop in E levels may actually lead to lactating (like a woman usually does after delivering), and there may be pain associated with that change.