I've had the same problems. But it is very easy to do when you have a bounding box, which can be determined from the GeoJSON (like meetamit said), or while creating the GeoJson. And the width of the wanted SVG.
I'll start with the variables lattop, lonleft, lonright, width
and height
for the bounding box of the geojson and the dimensions of the image. I haven't yet occupied myself with calculating a good height from the difference in latutude. So the height is just estimated to be big enough to fit the image. The rest should be clear from the code:
var xym = d3.geo.mercator();
// Coordinates of Flanders
var lattop = 51.6;
var lonleft = 2.4;
var lonright = 7.7;
var width = 1500;
var height =1000;
// make the scale so that the difference of longitude is
// exactly the width of the image
var scale = 360*width/(lonright-lonleft);
xym.scale(scale);
// translate the origin of the map to [0,0] as a start,
// not to the now meaningless default of [480,250]
xym.translate([0,0]);
// check where your top left coordinate is projected
var trans = xym([lonleft,lattop]);
// translate your map in the negative direction of that result
xym.translate([-1*trans[0],-1*trans[1]]);
var path = d3.geo.path().projection(xym);
var svg = d3.select("body").append("svg").attr("width",width).attr("height",height);
Note, if you go over the date line (180 degrees), you will have to take the overflow into account.
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