As a permanent US resident - you are required to report all your income worldwide.

Generally LLC is not taxable entity - all income should be passed through to members and should be reported on individual tax returns regardless it was distributed or not. Distributed income is likely self-employment income and 15.3% self-employment tax would be required.

If an LLC does not File Form 2553 - http://www.irs.gov/pub/irs-pdf/f2553.pdf , it will be classified, for Federal tax purposes under the default rules. The default rules provide that if the LLC that has only a single member and is not required to be classified as a corporation - will automatically default to the classification of disregarded entity. The disregarded entity files as a sole proprietorship and completes the appropriate schedules as part of the single owners Form 1040.

If the LLC is a sole proprietor for federal tax purposes, the entity should file

Form 1040 Schedule C, Profit or Loss from Business (Sole Proprietorship)

if LLC is expected to have a profit by the end of the tax year - members should calculate tax liability based on the expected profit. They should not wait till April 15 to pay tax liability, but should pay quarterly estimated taxes using form 1040ES - http://www.irs.gov/pub/irs-pdf/f1040es.pdf - otherwise they might expect additional underpayment penalty.

These estimated payments should include income and self-employment taxes.
Assuming that $60,000 is your net income (after deducting all qualified expenses) - your estimated federal tax liability would be

--- 15.3% self-employment taxes

--- 15% income taxes (assuming that you are in 15% - 25% tax bracket)

--- for DE tax purposes:

see for reference - http://corp.delaware.gov/frtax.shtml

All corporations incorporated in the State of Delaware are required to file an Annual Report and to pay a franchise tax.

there is no income tax if you do not conduct a business in Delaware.

Yes - that was the misunderstanding from my side - sorry.

So you would be a non-resident for the US and should report only income from US sources. Any income generated by the Delaware LLC is considered from US sources.

A single member LLC will automatically default to the classification of disregarded entity and income and qualified business expenses should be reported on member's individual tax return the same way as for a sole proprietorship.

As a nonresident you generally should file Form 1040-NR - http://www.irs.gov/pub/irs-pdf/f1040nr.pdf - and business income and expenses would be reported on the Form 1040 Schedule C, Profit or Loss from Business (Sole Proprietorship)

However according to US-Japan tax treaty - http://www.ustreas.gov/press/releases/reports/conventionfinal.pdf

Income that residents of Japan receive for personal services as independent contractors or self-employed individuals is subject to the provisions of Article 7 (business profits) of the treaty. Under that provision, business profits are exempt from U.S. income tax unless they have a permanent establishment in the United States.

So your business income would be only taxable in Japan.

The Delaware LLC is required to pay an annual franchise tax of $250.00 - http://www.state.de.us/revenue

No Delaware state income tax if the LLC does not do business in Delaware.

Although Limited Partnerships, Limited Liability Companies and General Partnerships formed in the State of Delaware do not file an Annual Report, they are required to pay an annual tax of $250.00. Taxes for these entities are to be received no later than June 1st of each year. - you may do payments online - http://corp.delaware.gov/paytaxes.shtml

I would also recommend Delaware Guide for Small Businesses - http://www.dedo.delaware.gov/publications/startup_guide/files/de_small_%20business_guide.pdf

As I mentioned above - a single member LLC will be classification as disregarded entity and income and qualified business expenses should be reported on member's individual tax return the same way as for a sole proprietorship.

So - that would be your business income - not salary or wages.

Attach to your tax return the form 8833 - http://www.irs.gov/pub/irs-pdf/f8833.pdf to claim a treaty exception - scroll down for instructions.

That income is your business income - there is no salary and wages.

Salary or wages would be paid to you if you work for someone. You do not work for anyone - and there is neither salary nor wages - but the business income from your self-employed activity.

here are some information on your Japan tax liability - http://www.worldwide-tax.com/japan/japan_tax.asp

An employee - as the individual's tax is deducted by his employer, there is no obligation to file an annual return for an income of less than 20 million yen per annum.
When an employee earns income from two sources, or additional income as a self-employed person in excess of 200,000 yen, he is obliged to file an annual return.
A self-employed person - is obliged to report and pay tax on income for the current year no later than March 15.
When the results for the previous year show a net tax obligation (as against tax deducted at source) of at least 150,000 yen, two advance payments must be made in the following year on July 31st and November 30th, each advance payment being 1/3 of the total net tax for the previous year.