You are confused about the terminology. Cost basis is the amount you paid for the shares when you bought them. The amount you sold them for is the proceeds of the sale. In your example, the cost basis is $3,000. The proceeds are $2,250. The $750 difference is a capital loss.
You can use the average basis method for mutual fund shares. For details of the rules see "Special Rules for Mutual Funds" starting on page 67 of IRS Publication 550, "Investment Income and Expenses."
