I think the tutorial popups are good. They convey enough info to guide the player, without being too much. The game is pretty intuitive, so it doesn't need much guidance.
The game is cute. I'm not big on idle/clicker games, really only having started to play them in jams, so my experience is somewhat limited. For the style it does feel like a good base, to me. The changes you've been making are making it feel more complete and enjoyable. I like the upgrades, it adds more to do and lets you keep unlocking things after adopting all the cats. The automation upgrades feel like an important addition. Since I I don't play a lot of this style I may be wrong, but it does seem like automation upgrades are a staple of the genre. I like the progress bars showing how long until the automation will complete.
I do think that it would be nice if after upgrading it would stay on the upgrade so that I can keep pressing the upgrade button. If letting they game go for a while and building up a bunch of cash I will often upgrade the same thing many times in a row, so not needing to go reselect the upgrade each time would be preferred. I know there was an issue before with free upgrades and deselecting was likely part of the fix, but staying selected and updating the info feels like it would work better.
With the automation it is far easier to simply leave the game up in the background, on a side monitor, or even in the corner of your screen as you work on other things. While I don't do it, I have seen that some people like to have companion apps open while they work. Having the cafe off to the side with the cats running around can work well for that kind of companionship app. I'm not sure if it would be worth it, or how much effort it would take, but something you may want to consider is having a mode where much of the UI is hidden and the view is reduced for that kind of sitting in a small window off to the side to watch the cats and customers. I wouldn't focus on this now, but just think about it for the future as a possibility depending on how the game grows.
The stats screen is another great addition. It is nice to be able to see the big total numbers for everything. The stats could use with some number formatting, such as thousands separators and 2 digits for cents. The money on the main UI could use it as well. While writing this out I left the game going and have made it up to Cafe Level 78, earning $350k.
I think the planned future addition of adding multiple cafes will be a nice growth of what you already have.
This was a nice upgrade. Everything feels better.