Portals might help, though it's fairly easy to add them by myself (thus accepting that hey won't into the look & feel smoothly).
I will put the pieces together in advance, at least mostly, because I need some special features for the map. It will have an entry point (stairs or such) on each side, a broad stair to lower levels in the middle, I want those portals more on the outskirts so they're not like to be stumbled upon and I want to block a direct way from the entry point to the middle stairs, so the PCs will have more battles to fight. So I have to do it in advance.
I'm not sure whether I'll use the smaller ones or the battlemat scale. I will dm this online, it won't matter that much. Will be a question of what fits easier into map tool and whether that is okay concerning file size, since my internet connection is fairly slow. But if I would dm this at the table, I'd be very happy to have them battlemat scale. It's just easier to do than resizing it on ones own. Same as having a grid or as in your case being able to tell where each grid is. This is even more of ap ain in the ass than having to resize on most maps. And I think for you as a author both are relatively easy todo (though it surely doesn't come for free). And maybe hopefully one day I'll be able to dm for some people at the table again and then I'll be happy to have some proper sized random dungeons handy.