Thanks for all the input! When I did the desmog, I used the stock pipe ends and filled with JB weld. When I started the bike and it warmed up, I blipped the throttle a couple times and had the S**T scared out of me when I heard this LOUD engine noise.

After my heart re-started I started looking for the source of the noise. Turns out I blew out the pipe ends on both the left AND right side rear positions. So, I am just going to put the caps in and finish off with JB Weld.
And tonight after work, I am going to pick up 4 of the 9/16" plugs from Car Quest Auto Parts....FINALLY !!!