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Rather than claim the prior year(s) donated property as a donation in the current year you should consider attaching a statement to reflect the reason that the current balance sheet beginning balances do not match the prior year ending balances.
That is a more accurate representation of the facts as you presented.
This is a method that is used fairly commonly since prior corporate books may or may not have been prepared with competent professional guidance. I have had to do this for solely owned corporations that became clients and have never had any dire consequences. After all, the facts are the facts.
The donations would usually be recorded at fair market value at the time of donation; but you will have to make a decision what, if anything to do with any decrease in value between the time donated and the time being record on the books.
It is not clear if Schedule O 990-EZ was or was not included in the past; but that might be a usual item to include with the statement explaining the change in the asset balance(s).
Please ask if you need clarification or have another question.
From your description it seems on the 990-EZ that line 21 Net assets or fund balances at end of year, line 24 Other Assets and line 27 Net assets or fund balances at end of year were all not correctly reported in the prior year(s).
Indeed, you should report the current year with the correct amount for every line that was not correctly reported in the past.
Unless the assets are used in producing taxable income (such as Unrelated Business Taxable Income) it is optional for most nonprofits to record depreciation on a tax basis and can just use book depreciation on From 990 Part IX - Statement of Functional Expenses. You have some freedom in depreciation methods unless you are claiming a tax deduction. I would likely not include prior allowed (but unclaimed) depreciation or might not even claim depreciation)
I hope this clarifies for you.
Please continue to ask, as you need.