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With regard to question 1:

From other postings where the amounts from the algorithm were less than  on line 3e, they were initially using the net gains from Schedule D.   When recalculated using the gross  proceeds, that corrected the difference.

 

With regard to question 3:

If TT generates a Schedule D, the default  “qualified dividends and capital gain tax worksheet” is replaced by the Schedule D worksheet.

The built-in algorithm is correct, and  the explanation for the “qualified dividends and capital gains worksheet” is correct, but the explanation for the “Schedule D worksheet” is out dated with respect to line numbers.  Using the Schedule D worksheet, here is a shortcut  to calculate the amount retained on 1l.  It does not include any amount in 1i or 1j, so if there are amounts in 1i or 1j, it will be an approximation.

The ratio:

(Line 30 x 0.4054) +(Line 33 x 0.5405)

              Line 2a

Multiply the result by the amount in 1h and that should be or close to the amount in 1l, the amount retained.  Subtract that from 1h and the result is in 1k, the amount  adjusted ; (reduced)