Your title gets error
Code:
! LaTeX Error: There's no line here to end.
using: LaTeX2e <2005/12/01>
Better:
Code:
\title{\rule{0.6\linewidth}{1pt}\\
\vspace*{2ex}
Computer Systems 2 \\
Journal\\
\vspace*{2ex}
\rule[3mm]{0.6\linewidth}{1pt}
}
However - it is doubtful that this is the cause of your output anomaly.
Even with the error, pdf output I get from your file does not show the page overrun that you see.
For me - "final thoughts" is half-way down page 2 ... the footer should be at the bottom. It is not clear from your picture how the page is filled up. However, when fill the sections with lorem ipsum to bulk it out, or even just vertical space, the page size is honored.
This means that the trouble is either in your viewer or TeXshop.
Unless you've been playing around with custom page styles?