After doing a scan for trojans on my dedicated server, through the security option on the WHM panel, I received several results.  I contacted the management team at ManageMyBox to make sure that these were not trojans and were in fact false positives.  Below are the supposed trojans found on my dedicated server:

Possible Trojan - /etc/cron.daily/logrotate
Possible Trojan - /usr/bin/cpan
Possible Trojan - /usr/bin/instmodsh
Possible Trojan - /usr/bin/prove
Possible Trojan - /usr/bin/psed
Possible Trojan - /usr/bin/pstruct
Possible Trojan - /usr/bin/s2p
Possible Trojan - /usr/bin/splain
Possible Trojan - /usr/bin/xsubpp
Possible Trojan - /usr/sbin/pureauth
Possible Trojan - /usr/sbin/antirelayd

This is the response I received back from the nice people at MMB.

Well you can ignore those, Those are not really trojans as they are system binary and perl files which are getting frequently modified by cpanel and other applications, so while doing a scan cpanel considers the most frequently modified system files as trojans. So there is nothing wrong with your server - Let me know if you still have any questions.

So, one idea down, on to more research to help make my server run a little bit more efficiently.  I think I have some scripts and MySql issues that are starting to clog my pipes, so anything I can do to make it more efficient I'm gonna try.  But for now, if you run into these being listed as trojans on your server, rest assured they are merely false positives.