Ineligible Prior Year's Roth IRA Contributions

[NSNM]

A married individual, 30, (status MFJ) filed Form 1040 for 2005, 2006, 2007.
With extension filed, Form 1040 for 2008 has not been filed yet.
Filers did not report ineligible excess contributions in those years.
Both spouses contributed to their company sponsored 401(K).
In each of the years, MAGI was much in excess of phase out range.
Therefore he was not eligible to contribute Roth IRA.
Prior to 2005 he was single, eligible and contributed to his Roth IRA since 1998.
He maintained Automatic monthly contribution to his Roth IRA with Custodian B
And lumpsum transfer from other investment account with Custodian A.
His contribution to Roth IRAs are as follows:

Year 2005 Custodian A ... $0, Custodian B ... $ 900
Year 2006 Custodian A ....$2000, Custodian B ...$ 1800
Year 2007 Custodian A ....$3839, Custodian B ....$1800
Year 2008 Custodian A ....$0, Custodian B ....$450

In 2008 he received distributions (Excess contributions) from Custodians and they reported as under:

Custodian A Form 1099-R (2008) Box 7 Code "J" $5839 (Basis)
Custodian B Form 1099-R (2008) Box 7 Code "J" $1800 (Basis)
Custodian B Form 1099-R (2008) Box 7 Code "JP" $1850 (Basis + Earnings)
Custodian B Form 1099-R (2008) Box 7 Code "J8" $474 (Basis + Earnings)

Custodian B did not return 2005 excess contribution of $900.

I understand that Part IV of Form 5329 has to be completed for each of the years starting with Year 2005, computing 6% Additional Tax on excess contributions NOT withdrawn and carrying the balance to the next year. This process continues for each succeding year until all of excess contribution is withdrawn and no tax becomes payble.

All of the basis are reported on Form 5329 with 6% additional tax. And earnings are reported on Form 8606 with 10% tax for early withdrawal penalty.

Question 1:
In the years (2005 and 2006) there are no earnings from excess contribution, could I simply file Form 5329 with a check for 6% additional tax, without filing Form 1040X or is it required to file 1040X for 2005, 2006 and 2007.

Question 2:
In which year's Form 8606, the earnings of $50 relating to 2007 excess contribution should be reported. Is it year 2007 or is it 2008 with ($50 + $24) combined earnings from excess contributions of 2007 and 2008.

Could anyone familiar with Roth IRA help resolve the issue. I appreciate and thank you for any response.

[JG EA]

Question 1.

In the instructions for 5329:

File Form 5329 with your 2008 Form 1040 or Form 1040NR by the due date, including extensions, of your Form 1040 or Form 1040NR.

If you do not have to file a 2008 income tax return, complete and file Form 5329 by itself at the time and place you would be required to file Form 1040 or Form 1040NR....

Prior tax years. If you are filing Form 5329 for a prior year, you must use that year's version of the form. If you do not have other changes and have not previously filed a federal income tax return for that year, file Form 5329 by itself (discussed earlier). If you have other changes, file Form 5329 for that year with Form 1040X, Amended U.S. Individual Income Tax Return.

So need X for those prior years.

[NSNM]

Thank you JG

I thought I have an option to file Form 5329 only. I was not sure about filing 1040X. Your confirmation of filing 1040X was helpful and thank you again.

From an earlier discussion on this subject dated 03/29/2007 Bill Tubbs brought the attention to Pub 590 (for 2006) pg 62 under "withdrawal of excess contributions" --
"THE EARNINGS ARE CONSIDERED EARNED AND RECEIVED IN THE YEAR THE EXCESS CONTRIBUTION WAS MADE".

So, I found answer to Question 2 as well. Thank you Bill Tubbs.