What are the advantages of using your custom engine instead of unity, unreal engine?
In addition I have complex, dynamic geometry to render. And I wrote a custom, fixed-precision integer math library to prevent rounding errors for the almost infinite game world. Other products have weird rounding errors near the start, the middle or end of their worlds because of inconsistent floating-point accuracy. Moving to doubles only mitigates the problem instead of solving it.
And then it's just efficiency too. I have no idea how or why Unity or Unreal will treat my assets. As demonstrated on the stream: the game instantly switches between visual styles and texture quality. It lazily loads all resources so the main thread is only stalled when doing bulk uploads to the GPU. This makes the game start up in less than a second, something I couldn't pull off with a COTS engine.
Let me know if this answer didn't address your question fully.
For Angeldust I've done dozens of updates, each and every single one building upon the existing base. Looking back it's amazing to see that the product evolved in an almost linear fashion from v0.0 all the way to the current version without ever having to drop or redo features. But because the product evolved as a whole I can not really distill a time estimate for only the "client side engine".
I mean: would you consider testing the client side engine part of client side engine development? For testing you need a working server. For which you "need" a working network simulator. It's dependencies all the way down.
And how about translation work for in-engine strings, updating shared libraries and frameworks, issue tracking, writing the asset conversion toolchain (which needs assets, which need integration). It's very hard to come up with any solid number. Maybe if you can severely limit your question's scope I can come up with an educated guess.
For the 3D world, start with a checkerboard pattern or so. In fact, this is almost exactly what I did to start Angeldust. I once showed off some early game prototypes on my stream, take a look at this one for example: https://www.youtube.com/watch?v=qMs8YpkSrg0&t=3289
If you keep watching that stream you'll see other in-progress versions so you can see how my product evolved.
Angeldust's physics are relatively straightforward since it's based on a voxel grid. All game world intersections are approximated using axis-aligned bounding boxes (AABBs). I wrote the physics engine myself from scratch to reduce the number of game world data lookups, because that's pretty much the hot path in the code.
In the YouTube video from my earlier comment you can see that initially I started out with just game world boundary clipping and simple plane physics on the checkerboard. As I expanded my game world model, the physics engine grew along. So my advice would be (again) to start simple and grow from there. You'll do fine!