Two stupid mistakes. Recently I was uploading a simple sketch to my Uno R3 to control a 12V RGB light strip. In the process, a loose jumper connected to +12V touching something it shouldn't (I didn't see what). Whoops! Long story short, that board went up in smoke, but the ATMEGA should be alright. Today, I have another Uno R3 which I tried uploading a similar sketch to after re-checking my breadboard for problems. I went to plug in the Vin to the breadboard (which would turn the light strip on), and I missed and touched the ground. How I make essentially the same mistake twice in one week is beyond me... My Mac cut power to itself as a safety measure, and I believe I ruined the ATMEGA. I was also worried that I may have fried my USB ports, but they still work with other devices such as my iPhone.
So heres my problem. After I got my computer up and running again, I unplugged Uno 2 from the breadboard and checked to see if I could upload a simple sketch. Nope, "stk500_recv(): programmer is not responding." I assumed the ATMEGA on Uno 1 could be used in place of the ATMEGA on Uno 2. I first removed the ATMEGA from Uno 2 and plugged it into the computer to check if the COM port was recognized. It was. So I unplugged it, put in Uno 1's ATMEGA and plugged it back in. Green light, COM ports show up, no heat (the old Uno 2 ATMEGA slowly heated up after the Vin mishap). All seems fine. However, when I upload scripts, I get "stk500_recv(): programmer is not responding."
I'm not sure what could be wrong. I'm assuming my USB ports are working fine because my iPhone is recognized by iTunes, and they still provide power to the Unos. I'm also assuming the ATMEGA from Uno 1 is undamaged. Could there be a hidden safety feature on my computer thats preventing communication to devices such as an Arduino? I have a 15" Macbook Pro mid 2012.