Part 4. Use LIFO or FIFO?
You can sell shares in the order you bought them - first in first out (FIFO), this increases the odds you will pay the lower long term capital gain rate, but you may have reasons to sell shares you bought most recently - last in first out (LIFO), for example, after you bought the stock, it tanked, allowing you to take a capital loss.
You can also specify certain shares to sell, or just assume you will use the average cost per share when figuring your basis. If you use the average cost per share to account for part of a position that you have sold, you need to use the same method when you sell the rest.
IRS usually assumes you use FIFO method, if you use a different method, you must let your broker know in writing and keep a record of that order in case the IRS asks about it.
Next, part 5 - tax on futures and options.