Matabele,

In wood it's just a matter of turning the screw to align, it's never more than half a turn to alignment. In metal to metal fits the shoulder of the screw/bolt head has to be shortened down or the pocket it seats into has to be deepened. I usually shorten the shoulder, this is why I leave the screws all long until I get to this point in the build, that way I can bring them all down to flush.

The fences and nipple seat are just a matter of patience and sand paper glued around dowels of different sizes. And for really tight spots, if you are really careful you can sometimes polish them with a pointed Cratex wheel on a Dremel...but I don't recommend this method as it is really easy to screw things up with a Dremel(it's a last resort tool for me if I can't get into the place with anything else).

Colin