If there’s an automation process I don’t know or use it. With Morrowind’s CS heightmaps can be created quite quickly by hand. A quick and ugly tutorial on how I do it:

-first, you need to have a (preferably topographical) map of your landmass with a visible cell grid (preferably with coordinates included so that you don’t lose track of where you are). This map should be open in one window, the CS in another.
-in the CS, load a cell at the edge of your first topographical level (in the simplest case this will be your coastline). Open the heightmap editor, and with a size 30 (largest) brush raise a patch of land to the desired height of that level. (In the case of the coastline, a short distance over the water line).
-switch to the flatten terrain brush and flatten the top of your raised patch of land. If the height difference between topographical levels is too large, flatten terrain doesn’t work, so you’ll need to insert an additional level between them.
-now trace the outline of the topographical level cell by cell. More detailed features can be achieved with a finer brush, or you can just leave them for later in the process.
-once you’ve traced the outline of the level, fill it out. Technically if you’ll be adding another layer on top anyway you won’t need to fill all of the lower level out, but given the above limit on the flatten brush that won’t always work.
-having filled out that layer, repeat the process for the next one.

For features like rivers, I generally lower terrain down to the desired depth and then just use a brush of the desired thickness to trace the course of the river. I’d also use a similar approach for lakes, unless you want a really deep lake, as the distance between topographical levels (especially if those levels are the coastline and the default ocean floor) is too large for most lakes.

By the end you’ll have your rough heightmap. From there, use a mixture of raise terrain and the smooth tool to graduate the transition between topographical levels as desired and in general add detail.
Once you’ve got the hang of this approach, you can create a heightmap of the dimensions you’ve specified within a few hours. (I managed to knock out the Narsis border and rivers, together probably roughly comparable to your coastline, well within a day). Barely any time compared to the actual detailing work.

I hope this explanation suffices; otherwise I could try tossing together some images for purposes of illustration. Might not be a bad tutorial for the site, actually, even if for the purposes of TR I doubt it will see much use.