I'm sure there are other ways to solve this, but I replaced the 3 header pins that were in the way with 90 degree angle header pins and it gives me just enough clearance to mount the LCD properly. I would only encourage you to do this yourself if you are comfortable unsoldering/soldering, otherwise have someone you know who can do it for you so you don't damage your shit.

20131002_203335.jpg 20131002_203244.jpg

I picked mine up at a local shop near work, but these are very common parts. You can get these from Ed at GPE, Digikey, Mouser, etc or possibly a local shop like Fry's.

These are for the 2 smaller rows of header pins (.100):
Product ID: 69191-509H
Connector, 0.1" Header, 9-Pin, Right Angle
http://greatplainselectronics.com/Category-74.asp
You'll need to get a couple and chop em down to be 7 pin and 8 pin that you need.

These are for the 1 bigger row of header pins (.156):
Product ID: 26-48-1246
Connector, 0.156" Header, 24 Pin, Right Angle
http://greatplainselectronics.com/Category-79.asp
You'll need to trim it down to just the 7 pin that you need.

If it's not sitting flush against the foam around the window, then it's not installed properly (according to the instructions) and the LCD is recessed a little further back. The white spacers that came with it are supposed to be installed first, not the original black spacers. If you're ok with it, then there's really no need to change it, seriously. Some people are nit picky about stuff like that with their games, like me