The piece of wood or metal that strikes the hopper, presumably to stop the hopper from clogging up with flour, is called the clapper, but here I think the clap is simply the lid of the box that the grain is poured into. Hence lifting up the clap is the equivalent of lifting up her dress or smock, to put in his 'chiefest grain'.

The reference to the dam and holding back the water can surely only mean the lubricating love juices produced by the girl. Only when this is released can the operation really get going. As someone has said both operations produce friction. It could possibly mean that in both cases water is needed to cool them down. These double entendres are rarely precise especially once they get into oral tradition.

As for that last line 'ye may all come and lick' yeuch! Think about the last line of some versions of the crabfish 'There's an apple up me arse and you can have the core' for something similar.