No, do not breakout the costs of the new flooring or HVAC. These costs get added to your property basis. IRS Publication 527 says
To figure your property's basis for depreciation, you may have to make certain adjustments (increases and decreases) to the basis of the property for events occurring between the time you acquired the property and the time you placed it in service for business or the production of income. The result of these adjustments to the basis is the adjusted basis.
You are correct on adding the painting to the cost basis as you cannot expense this now because the painting occurred before you began renting out the property.
If the flooring or HVAC was done after you began renting the property, then they would be listed as separate assets.
