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When you sell you file a form called 4797. On that form you enter the original cost, the cost of improvements (and maybe some other stuff). You also enter the depreciation "allowed or allowable" and selling expenses. From which a gain or loss is determined. If you failed to take depreciation you were entitled to take, you can take it now in one (or both) of two ways. for the 3 prior years (before 2000) you can file amended returns and take the depreciation that way (and get a refund on those prior year returns). If you failed to take depreciation more than 3 years ago, you can file form 3115 and take ALL the depreciation on the current year return.

But, alas, I am ahead of myself. You asked for advice.
The advice here is, of course, free, and sometimes is worth all of that. This advice is priceless. Go hire some help. There is clearly a lot that you do not know about "schedule E". And what you don't know has already cost you a bunch (much of which you may still be able to recover). Don't let your ego put you in the poor house.
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