Hi all and again thank you in advance for reading this and hopefully helping me out.

To generalize this let's say there was a loss of 100k from stocks. Then a Home Sale was completed to which resulted a capital gain for the primary residence of 1,000,000. Married filing jointly 500k so taxable capital gain of 500k. Schedule D automatically subtracts the whole 100k loss from stocks and results in a 400k capital gain instead of the 497k (3k/year net capital loss from stock). 

Can anyone help?