What do I report for an LP in a Roth IRA?

[Critter-3]

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. 

[mlu056]

Thank you very much for answering my question. I get that my 1040 does not connect to the 990-T now. But what is 990-T, why am I getting hit by this Tax just investing in the ET stock? I'd appreciate it if you could explain a bit.

[Critter-3]

https://www.irs.gov/charities-non-profits/unrelated-business-income-tax

[TomD8]

When unrelated business taxable income ("UBTI") is earned by a tax-exempt entity such as an IRA, and the total amount earned is $1,000 or more, the IRA must file Form 990-T, and any resultant taxes must be paid by the IRA.

Normally the filing of Form 990-T and the payment of the taxes is handled by the IRA custodian.

None of this is reported on your personal tax return.  It is all handled within the IRA.  No 1099-R is issued for these transactions.

Usually UBTI is earned by Limited Partnerships or Master Limited Partnerships that are held by your IRA.  When an IRA owns an LP or MLP, it becomes a partner in the partnership.  Hence it shares responsibility for the taxes due on the partnership's unrelated business income.