Forgot about this thread, but here's an update.
I have 10k miles on the car now and everything is very smooth. I don't notice anything out of the ordinary now. It's been fine for a while now.
The clutch pedal did make some noise every so often...just a click every time I pressed the pedal down. I haven't hear this for a while either.
I suspect it is either the car going through break-in or it was the colder temps we saw during winter.