Retirement tax questions

  1. My account is ROTH IRA, do I have to pay tax on gains from trading ET stock?  NO ... nothing that happens inside an IRA is reported on your personal income tax return.
  2. If I do, why does TD Ameritrade file 990-T for me, can I file it in my 1040?  Sorry but if the IRA was required to file the 990 form because of "unreleated business income"  (and had to pay  taxes on it)   again has nothing to do with the form 1040.  As already mentioned the IRA custodian should file this and send you a copy of it for your records nothing more.  Having these types of investments in an IRA is usually not a good idea as you can see.
  3. Is the money TD Ameritrade is taking out from my Roth ira account just tax withheld? Can I file a 1040-X to claim back the overpay part and put it back to my Roth IRA, because my calculation shows TD Ameritrade pays more than I should?   Once again what happens inside an IRA is not reported anywhere on the 1040 at all.  If they send you a 1099-R for the distribution to pay the tax is it NOT considered withheld taxes and cannot be reported as such on the 1040.  You may  have the option to pay the taxes with non IRA funds (check with them) however they are still not deductible on the personal 1040 in any way ... buy using funds outside of the IRA it preserves the investment inside the IRA so this is a decision you need to make for yourself.  Either way none of the 990 taxes are deductible anywhere in any way.  Thus are the rules for IRAs ... you get some tax benefits from investing in them however they also have drawbacks especially if you invest in LP's like these.