I know the amount I paid for the house (second home) minus the repairs and improvements. Can I just use the actual amount gained for my net proceeds?
Your down payment has nothing to do with basis. The only things considered are purchase price, adjustments to basis and sales price in any transaction. You would not look at cash in hand or consider mortgages.
For basis adjustments see the link below.
https://www.irs.gov/publications/p551/ar02.html
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