I actually wouldn't offer to pay for the dress. If the bride was buying it from a shop... maybe? But her aunt is making it so it probably won't cost the bride much money and it is her choice to have your daughter as a flower girl. If you feel obliged to offer I would ask something along the lines of 'would you like me to pay for the fabric?'.

I think a home made card or a picture from your DD to the bride and groom would be lovely.

As for the wishing well... if you would prefer to buy a gift you should do that and I would hope that the bride and groom will accept it graciously. Several years ago DH and I went to a wedding with a wishing well. We put $100 in an envelope and placed it in the well without our names. I figured that's what you did, just like you would remove the price tag from a wedding gift?? We also left a card on the table next to the well with some heartfelt words. I noticed that some people had done the same as us, some had put signed cards in the well (I assume with money in the card) and some people had put cash in the well, no envelope or anything. Anyway, we never received a thank you for attending the wedding which I thought was a little rude. Turns out that the bride and groom only sent thank you's to the people who put cash in a signed card!! Because we didn't put our names on the envelope with the cash they assumed we didn't give them anything apart from the signed card - which should have been enough anyway!! So... we no longer see that particular couple and I loathe wishing wells!!!