Thanks again, @baldietax ! I decided to cross check my federal taxes in FreeTaxUSA as I've seen that product widely recommended by others on some forums I participate in. To my surprise, it was clearer and much more user friendly and we will likely shift over for next year.
Running my numbers again in FreeTaxUSA helped me see that what I think is going on is that the tax programs take into account the allowable annual loss (-$3,000) and HSA contributions so those are not part of what a user should enter. In my case, for each quarter, I only need enter all income (interest, dividends), IRA distributions (Roth conversion), cumulative losses or gains incurred over each quarter, qualified dividends and a couple other things smaller items like foreign tax credit, etc. Turbotax and FreeTaxUSA will do the rest for the calculation.
By doing this I was able to reduce my penalty to zero.
