Yes. The specific identification method allows you to use the cost basis of the shares you sell to figure your gain or loss. FIFO, or first-in, first-out, is the default method for figuring basis if you do not instruct your broker or agent to use the specific identification method. You can override FIFO at any time buy giving directions to your broker; get a written confirmation that you are using the specific identification method.
This is generally adjusted gross income increased by certain items such as tax-free foreign earned income. MAGI usually is used to determine phaseouts of certain deductions and credits.