Just an update. Like I mentioned above I upgraded the chainring to the Sugino Messenger, which also required me going to a 1/8 chain. After putting about 15 miles on the bike with new setup the chain feels much better. Yes there are a couple of spots that are slightly tighter, but is much better than before.

Now, I just need to up the rear cog 17T (knees) and 1/8"