The first section of the OP is a generally good characterization of Atheism. However both points you raised are not "Achilles heels" of Atheism at all....
First Part - Matter and Mind
Thoughts, concepts and whatnot are a result of brain chemistry and electrical impulses in the brain.... Therefore, it is indeed just matter and energy. There's nothing transcendent about it.
This whole section is just one big appeal to emotion, and therefore invalid.
In short, it doesn't matter if you
want there to be an ultimate meaning to everything, it doesn't affect the reality of it being true or not. Simply believing in your God because it feels good and you can delude yourself is not compelling.
Things have meaning because we place value on them. I value my relationship with my friends and family. I value the things I like to do, I value myself and many other things.
The fact it's likely going to end someday doesn't affect how much I value everything. On the contrary, it makes all those things even more valuable.
Personally, what I think is bleak is your viewpoint. If you think your life is meaningless without your God, that is a very depressing position indeed.
You haven't displayed how either one of those is an emotional appeal... One is an argument built on a faulty premise, and the other is the appeal to emotion fallacy. Sorry, but that's not an Achilles Heel in the slightest.