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An LLC is a disregarded entity for tax purposes. Thus, the reason for electing sole proprietorship, C corporation or S corporation status. Since you have elected S corporation status for 2012, my opinion is to follow the advice of the accountant you spoke to and file the 1120S for 2012.
As to 2013, you will want to file Form 8832 (Entity Classification Election) to elect sole proprietorship status but it cannot take effect more than 75 days prior to the date the election is filed and it cannot take effect later than 12 months after the date the election is filed. However, you may be eligible for late election relief in certain circumstances.
The following is the link to Form 8832 and its instructions:
My suggestion would be to include a letter with Form 8832 explaining that you made a mistake in electing S corporation status, and that you have filed your 2012 1120S.
As to the "reasonable salary," I would not worry about it in your situation.
As to the expenses, the following article contains excellent information regarding startup expenses:
Please let me know if you require further information or clarification. I will be offline for a while, but if you have follow-up questions, I will address them when I am back online. This will allow you time for review the links I have provided.
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