d3-map | Map of Brazil using d3.js | Map library

Not sure if this is what you want but here goes:

below code works...

Your map is drawing as expected.

Let's look at the projection:

You are right, the error is in the projection. But, the error depends on if your data is projected or unprojected (lat long pairs).

If you have data that is in WGS84 - that is to say lat long pairs, then you have this problem:

Using your projection, but changing only the data source I get something like this (I shaved off the empty ocean on the right):

To center a Mercator properly, you need to know the center coordinate of your area of interest. This generally can be fairly general, for Switzerland I might try 47N 8.25E.

Once you have this coordinate you need to place it in the middle. One way is to rotate on the x axis and center on the y:

Strictly speaking (as of August 2017), no. The size is fixed within the tile module:

Computes the set of 256x256 quadtree tiles to display given the current layout extent, scale and translate. (API docs)

And Mike states:

It currently is limited to 256 [px] (discussion)

However, as coincidence has it, work is occurring to address multiple tile sizes.

See the discussion here. In fact, it seems that a possible implementation has been developed, see this thread, and this block for an example using the possible implementation.