A and B are very similar. The only difference is that, with A, the fee is added to the mortgage and a little more interest will therefor be paid while with B, you pay the fee now and no interest will be added to the £999 (unless you need to borrow to pay the fee). If you borrow £999 to repay at the end of 5 years at 4% interest, then you will need to repay £1169 in 5 years time.
The difference with C, in money terms, will be about 0.2% of the total, or £200 per year, which, over 5 years, is about the same as the fee. However, this extra will be added to the debt piecemeal over the 5 years rather than on the first day.
My preference from these options would be C, but the difference is small.