Hi. My name is*****'m looking at your question now and will post my answer or ask for more information here in a short while.
Given that the outbuildings were derelict when you bought the property, I'm assuming for an all-inclusive price, and that planning permission didn't exist at the time of purchase, I would have thought that only the land on which they sat had any value and that would have been reflected in the original purchase price. If I were you, I'd consult a land valuer for guidance as to the apportionment for two reasons:
1 A good land valuer will have had previous experience of the division of the original purchase price between the farmhouse and any part of the land or outbuildings used for business purposes of some sort or sold off for development. He or she should have an idea of land values at the time of the original purchase.
2 HMRC will almost certainly refer your calculations to the District Valuer who will make the same assessment of how the original purchase price should be split which may be different from yours. You would then need an expert (a land valuer) to argue your case.
Running a holiday letting business is seen as a "proper" business whereas letting property generally is not. Therefore, if you sell a furnished holiday let, you should be entitled to entrepreneurs' relief which will limit any CGT charge to 10% as opposed to the regular rates of capital gains tax applied to non-business assets or business assets where the qualifying criteria for ER aren't met by the business and/or its owner. As you appear to have been trading as a sole trader to date, adding your wife to the deeds of one of the properties will effectively turn your business into a partnership. Transfers of assets between a married couple who are living together are treated as having occurred on a no gain, no loss basis so she would take half your cost as hers. In order for your wife to qualify for ER on her share of any gain she will need to have been part of the business for at least a year before the sale of the business asset, the property and any goodwill which may exist. Take a look at HS283 here for information on ER.
I hope this helps but let me know if you have any further questions.
On your first paragraph, I agree.
If you sell the holiday let as a normal residence, you should still qualify for ER as you are effectively selling part of your business. What the new owner does with it is irrelevant. I'd try to run it as an FHL for as long as possible up to the sale. Look here for the FHL rules. You will then have one furnished holiday let left and the business will end naturally when you sell that one.