Jason Davies wrote an implementation of the conrec algorithm that does exactly what you need:
https://github.com/jasondavies/conrec.js It's got a working example inside
I believe that the white stripes are happening because of the projection you are using;
In fact the height of each rectangle should adjust accordingly going north and south from the Equator, because the Mercator projection alters the distance going north and south.
To have a fixed height of the rectangles you could try with this projection instead:
which preserves the dimension going north and south
It sounds like the problem in your case is the data. What you would need to do is take the original data and interpolate it to a smoother form. For this, you can use a GIS program such as QGIS. How exactly to do that depends on what format your original data is in.
Once you have the smoother data, you can plot it again in D3. My guess is that the end result would be somewhat similar to what I've done here, where contour lines are drawn to much the same effect as what you're aiming for.
Maybe you could take a look into heatmap js.
Although is point based it may give you a hint. It uses canvas instead of svg.
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