One of the frustrating things you'll find, is that there are varying opinions on what a Stroker is, or how to do it "right". So make sure you look at multiple writeups, and there are significantly more of those in the Jeep world.
If you'll be using that 4.0 head on a 4.0 block (with 4.2 crank and I think a cam that is not stock in either but made for strokers), then I'd expect/guess/assume that with a 4.0 head on a 4.0 block that it's a given that you'll need that coolant flow that was welded shut. And I'd expect you want to match the same shape & size too, and you may need to grind out all of the weld material that is up those passages, else the resulting turbulence could reduce flow. Do your research on polishing those passages, as sometimes a non-polished or specifically textured passage will have a higher fluid flow due to that textured/rougher surface holding a boundary layer of fluid, which resists fluid flow less than a polished surface that has a low or no boundary layer.
With the extra power/heat a stroker will be outputting, I wouldn't want to have reduced coolant flow. Look at a 4.0 block for the match to those triangular openings.
When I was looking at differences in the various 4.0 heads, I remember being surprised at needing different intake manifolds? I may not be remembering that correctly.
And there are differing opinions on which 4.2 crank is best or even works in a stroker. Early? Mid? Later? You'll have to confirm what that is about. And this is obviously the correct time to get your crank checked by a machine shop for true, etc.. Don't drop it!
I've not built a stroker, and it's been a number of years since I looked at doing so, so I can't give you my opinion of what is best... lol