Hello Jason,

Your signals look like snippets of RC6,  see http://www.sbprojects.com/knowledge/ir/rc6.php
and http://www.pcbheaven.com/userpages/The_Philips_RC6_Protocol/.
In any RC6 mode the signals should be the same length you were correct in your suspicions
of the signals displayed by xmode2, you need to get a consistent signal before proceeding.

You don't give details of your receiver but all times in your .conf file are multiples of 50 microseconds,
irrecord is not good at determining the timing data with this resolution it may be worth trying to start
with a template .conf file with the timing data provided..