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These new additions are nice,  they help keep track of certain things better.  There's a couple small problems though.

It seems like the buttons are behind the  "clicking" part of the screen, because I can click on them and even if I can't afford something, it still counts as a click and raises the gold as if I was clicking in the main area.

Example - If I click on Reset, it counts as 1 click, if I click Yes to reset the game, it starts over and I already have 1 click instead of 0.

You could fix this, by "greying out, or masking the buttons" until you can afford to buy something.  I'm not sure how you would do that with the "reset" button, unless you put it in front of the "click" area.  

Seeing that you have the background green, you could always have the buttons light up green around the outside of them, when you have enough gold to buy certain things ? It's your game though, so make it how you want it.

You already know that "secondes" should be  "seconds"

Playtime:   At level 1, it only goes to 59 seconds then resets back to 0, until you have 1,000 or more clicks.  After that, it will only count to 2 minutes 59 seconds, then resets back to 2 minutes 0 seconds.

Playtime is connected to (Total clicks) AND (Level).  After 1,000 clicks the Playtime only goes up to 2 minutes 59 seconds, but after I got level 8, it now goes to 6 minutes 59 seconds?

If possible, just make the Playtime separate and have it as a standard "number counter", it should work properly that way, since it wouldn't be connected to anything.

Total clicks:  works properly

Best clicks per second:  this works properly also, but you may want to hide this in Achievements or somewherre else, because the number only shows your fastest click and doesn't do anything else. You could just remove it and add an achievement for 5 clicks/second or 10 clicks/second if you wanted.

Current clicks per second: works properly

Screen breathing - The normal respiration rate for an adult at rest is 12 to 20 breaths per minute.

If you slow down the screen "breathing" by a little (maybe 16/minute) , it would have more of a relaxing effect while playing. I think you have it going 19/minute? Don't make it TOO slow though, you don't want relax too much and fall asleep while playing it lol.   But like I said earlier, it's your game, so do what you want   :)

Edit - If you want to work on your other game or different things I don't mind.  You don't need to keep working on the game just for me lol. I've been on here playing games and helping people fix bugs now and again, like I do over at Deviantart and other websites.

If you really wanted me to help, I have many ideas. Each time you gain a level, you could add a swirling line around the very middle, like an actual Atom. Or, after so many clicks (every 500 or 1,000), have the smoke trail coming off the mouse explode and change to a different color. I could come up with a lot of different things.  You wouldn't want to have TOO many things on the screen flashing or going too fast though, because certain people could have seizures.