Serial Monitor issues

Hello all my name is Brian and I am very new to arduino, circuits, and programming. Long story short, I am trying to build a gps tracking system for a weather balloon. I have had a variety of results with this. I am following Paul McWhorter's lessons on his website, writing my own code as he demonstrates. I have also copy / pasted his code at times to trouble shoot my own.

I have got my GPS hooked up, and last week week I had it writing NMEA sentences to the serial port. I was beyond thrilled to just have that working. Since then I have written code to have the GPS write to an SD card. Now I cannot get the GPS to write to that, and I cannot get it to write to the serial port either. I am using the adafruit GPS unit.

I do not know really where to even begin investigation. My first thought was the code, so I copy / pasted McWhorter's code. Still, nothing. I also left the GPS on for about 40 mins before checking it. (The first time I got it to work this is what I did and eventually it just started working)

I am very confident that my circuit is connected correctly. I also have the baud rate set correctly. What should I check next? Is it possible that the cord connecting my arduino is just bad? There are times when my code will not load the first, second or third time I try.

Thank you very much for your help,
Brian