Update

This ended up being a mess. It's a month since me initial post. I ended up having more knee pain and had to see a doctor. I'm doing a little light PT right now and I'm supposed to stay off the bike for another week. The doc says the knee was muscle related not tendon related. I'm getting a fit next weekend. The guy I set up the appointment with said just from looking at me he thinks I'm riding a bit bow legged.

As far as the achilles goes the stretches helped and it's healed I think. It may have been from a high saddle but I found some other things that may have caused it. I adjusted the tension on my SPD clipless pedals, I think they were too tight and unclipping over and over could have pulled on that achilles. In fact the one that hurt is the one I unclip the most. I also found my cleats to be a little far back, I think that cleat position could maybe affect how you move your foot during pedaling and that could cause achilles tension.