OK, I get it now, you're putting the components face-down. That's easily done.
BTW, I do an interesting thing with those headers if I want less clearance. I push the pins through the plastic holder about the length of the holder so the pins are shorter on top. I solder then in, trim them, and then pry off the plastic holder. I get an additional .1" of clearance that way.
From this view, there looked to be plenty of clearance on the top, the tallest thing here should be the transistor at around 1/4". I always like the board to be components up if I can, it's a character flaw. 
However, it's no problem to swap it so it's components down.
