This is why you don`t Incorporate (LLC) in other states. Whatever you do, do not file that application if you`re in a different state "USE THE ADDRESS OF THE STATE" you incorporated in, I think you just shot yourself in the foot, you have to open a Virtual Office in Nevada, before you file for your EIN so you don`t have to Register your business as a Foreign Corporation in the State you are doing business in.
Here is what you need to do before you file for your EIN,
1. Have a Virtual Office in Nevada - There are companies that will do the following for you: give you a Phone number, a receptionist to answer the phone for you, open a bank account for you in Nevada, and they give you 8 hours a year to hold your minutes (meeting) I think the price for that is 1,500.00 a year...
2. Once you have done step number one, then apply for your EIN...
Why did you open a Nevada LLC, when you don`t live there.... you just complicated things for yourself and your Accountant
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When starting your own business the need to "know-how" is greater than money!