Note: removing the battery can cause a hitch with OS X 10.9 Mavericks installation to a blank drive, or at least it did for me.
Disconnecting the battery makes the hardware clock reset to something like Jan 1, 2000. This causes the Mavericks installer to fail its self-check with the error message: "This copy of the Install OS X Mavericks application can't be verified. It may have been corrupted or tampered with during downloading."
To fix this, you need to open up Terminal from the Utilities menu in the bootable OS X installer environment and use the `date` command to set your Mac's clock back to the correct time before proceeding with the "Install OS X" menu selection, as described here: http://blog.mconserv.net/2013/10/install...
It might be a matter of how the screws are driven in, and not that they're slightly different sizes. When I reassembled my MacBook, a couple of the screws, including the one over the optical drive you mention, were hard to drive in and jutted up a little bit instead of sitting entirely flush. Swapping screws didn't help. The solution was to unscrew them and drive them in at a bit of an angle - perpendicular to the slightly curved surface of the back plate where the screw holes were, instead of fully vertical with respect to the ground the Macbook is sitting on. Doing it that way, the screws were easier to drive in and they all ended up flush in their holes. Didn't matter which screws they were. (I swapped a few around just to check after reading this.)