The running start is what reduces the fall due to gravity from 13.7 feet to 5 feet (or 4). You can't count it twice. The rate of vertical descent increases that vertical descent speed (v0sin(2)) by gt where g=32 ft/sec2 and t=time in seconds. The time, t, is horizontal distance/horizontal speed.
I am not counting anything twice. If the fragment already has a vertical velocity, gravity adds to it.
Regardless, the difference in our thinking is your lack of applying the air resistance to the fragment after it ricochets off of Elm Street.
We already established that simple geometry and a 2-degree downward ricochet angle reduces the amount of drop necessary to approximately 47.64” (12.7’-8.73’). Your claim that the fragment has to be going at a drastically reduced speed to have the time necessary to drop that far does seem to be correct. However, your claim that the necessary velocity and energy loss would have to be due to the collision with the pavement on Elm Street is not correct. The reason it is not correct is that you have not taken into account the air resistance force on the fragment after it ricochets.
I believe that I have figured out a few things about the ballistic calculators. And I have found a different ballistic calculator that shows more information. Here are a couple of images that show how the air resistance affects things.
First, here is a table showing how quickly the velocity and energy values are reduced. The distance from the mark on Elm Street to the manhole cover we have been using using is 250’ (~83.33-yards). Based on that, and looking at the table, we can see that after a distance of only 16-yards the velocity is already reduced by about half of the initial 1500 fps. And the elapsed time is only about 0.05-seconds. Wow, that is due to the huge (your word) effect of the air resistance particularly during the trans-sonic stage. And this already solves the “mystery” of a lot of our differences.

Next are some graphs. I have determined that the “level” line at the top of the top left graph represents the line of sight. I have set the height of the “rifle” sights at zero above the bore. Therefore that line represents sighting through the bore of a rifle aimed at 2-degrees below level (the same as the direction of the ricochet off of Elm Street). So the necessary drop is ~47.64”. The ballistic calculator indicates a drop of ~46.8”. Therefore we are within an inch and that should be close enough for the purposes of this discussion.

I hope this helps you understand the importance of accounting for the air resistance. And that the needed reduction in the velocity and energy of the fragment is not totally due to a loss at the time of the collision with the pavement on Elm Street. If this were taking place in a vacuum, yes; but not in the atmosphere in Dealey Plaza on 11/22/63.