Before you try drilling holes as Rob suggested, why not try to utilise the existing holes? You need to block them anyway, so you might as well stick a bolt in there and then cover it up with wax or plasticine.
Also, you said you made the flanges too large? What resin process will you be using to make the part? If you are doing infusion and the flanges are in the glimpses I can see of your mould, then those flanges aren't big enough. If you're doing wet lay then it will be fine, but for infusion I wouldn't have a flange any narrower than 10cm.