So when it is asking if I stopped using this item for business purposes in 2021, should I answer yes or no?
Answer YES.
It then asks for the actual acquisition date which was back in June 1996 when I purchased as a primary residence and then converted to full-time rental in June 2003.
That date "should" already be filled in. Leave it alone or you'll completely skew the depreciation history.
After I enter the details of the sale, a question pops up asking if I used this rental property as a personal residence any time after May 6, 1997 (not sure how this date came about), which I was still using as personal residence up until June 2003. Should I still answer no to this question?
I don't know why you're being asked that question. Typically, you would only be asked that question if you qualified for the "Lived in 2 of last 5 years" capital gains tax exclusion. You don't qualify for the exclusion since the property was not your primary residence at any time in the last 5 years you owned it, counting backwards from the closing date of the sale. Perhaps you incorrectly selected the option to indicate that "this includes the sale of my primary residence" maybe?
