But if we change Premise 1 to “Whatever begins to exist has one or more causes of its existence,” then the Kalam fails

If we use this alternate premise, we can still get one cause by applying Occam's razor. Simpler explanations are better all else being equal, so there is only one cause unless we have reason to think there's more. With the tree, we have reasons to think there's more. With the universe, we don't.

A substance is fundamental if everything else is made up by it. So if you believe that everything that exists is made up of mind, and matter at the most fundemental layer, then mind is fundemental and matter is also fundemental.
.
If you believe that they are both fundamental, then they cannot be made up of the same thing(s) otherwise that thing would be the fundemental thing, that grounds all of reality.

What is a substance and what is a property?

substances are the foundational or fundamental entities of reality.so if you believe that there are two fundamental entities of reality, mind and physical, then the argument is aimed at that.