1. This depends on your cash flow needs & preferences. I don't have a good answer as I am not at the point of needing to do this yet. :)
2. Yes, Vanguard will send a 1099-B at the end of the year if you sold any shares. You'll also get a 1099-DIV for any dividends that were generated from your investments (not related to selling shares). Dividends and capital gains are two different things, so you may want to be sure you are comfortable with the terminology. If you're withdrawing from a 401k or IRA, you'll get a 1099-R.
3. Depends on how much taxable income you have for the year. 4% of a $500k portfolio would be only $20,000, which is going to be a pretty low tax bracket, if not zero, assuming you have no other income (depends on several factors including your deductions, exemptions, capital gains tax rate, etc.). Obviously the answer may be different if you end up with $50k or $100k in income.
4. You are being taxed on the capital gains of the shares you sell. You will own some number of shares of each of the index funds in your portfolio, each bought at different prices over the years. You are being taxed on the difference between the price you sold it for and the price you originally bought it for. In most cases, these will be long-term capital gains (shares held more than 1 year), which under current U.S. law are taxed at a lower rate than short-term capital gains or regular income. Note, what I've written up to this point presumes all your investments are in a taxable account. If some of them are in a traditional (non-Roth) 401k or traditional IRA, the rules are different. In that case, you are taxed on the entire amount of your withdrawal (because you didn't pay tax on the money going into those accounts in the first place). For a Roth 401k or Roth IRA, you won't pay any taxes on withdrawals at all.
Hopefully this is all making some sense. Feel free to ask follow-up questions!