As for adding lines between the box plots, here is a hacky solution that works ok. Would probably need some work to make it general.
Assume we have the domain (['1A', '1B', '2A, '2B', ...]) in a variable called domain.
We can add a pretransition handler that draws lines after every second box:
function x_after(chart, n) {
return (chart.x()(domain[n]) + chart.x()(domain[n+1])) / 2 + chart.margins().left + 7; // why 7?
}
chart.on('pretransition', chart => {
let divide = chart.g().selectAll('line.divide').data(d3.range(domain.length/2));
divide.exit().remove();
divide = divide.enter()
.append('line')
.attr('class', 'divide')
.attr('stroke', 'black')
.merge(divide);
divide
.attr('x1', n => x_after(chart, n*2 + 1))
.attr('x2', n => x_after(chart, n*2 + 1))
.attr('y1', chart.margins().top)
.attr('y2', chart.margins().top + chart.effectiveHeight())
})
This uses the D3 general update pattern to add a vertical line after every other box (specifically those with odd index number).
It takes the average of the X position of 1B and 2A, 2B and 3A, etc. I have no idea why I had to add 7, so probably I am missing something.

demo fiddle.