As I understand your post, you have a problem - and it's not a small one.
If these property improvements were done before the property was a rental, or while the property was a rental, they should have been included in the assets/depreciation section when you converted it, or when the improvement was placed in service. If you did not do that, then you have an issue with depreciation recapture.
Property improvements to rental property are supposed to be depreciated from the date they are placed in service. If you did not depreciate those assets, then when you sell the property you are still required to recapture "and pay tax on" the depreciation you "should" have taken. While taking depreciation may be an option, recapturing that depreciation upon sale of the property is not an option - it's required.
If your state also taxes personal income, then you've got a double-whammy here. You should seek professional help for this so it's done right. Doing it wrong can be significantly more costly than the cost of professional help.
No, you can't amend past returns to fix this. It requires IRS Form 3115 to be filed. While the TTX program does include the 3115, it is *not* simple by any stretch of the imagination. Therefore, you should seek professional help yesterday, if not sooner.
