That God can cause a donkey to speak simply presents no difficulty because God is all-powerful. It only becomes difficult if we erroneously presuppose that either (1) God doesn't exist, (2) God is bound by natural law, or (3) God doesn't work miracles. All of these presuppositions are false. God does exist - He was seen, heard, touched and even nailed to a cross for our sake. And though He was subject to natural law in the person of Christ, He's not bound by it, for He made it.
Whenever we're presented with a miracle in Scriptures, we should always remember that God is the one who makes the rules. Not nature. Nature is a product of God. The fact that God does something that is contrary to nature is for the very purpose of signalling His divinity to us. So, very simply - when we learn about God doing a miracle, it's sufficient to ask yourself: Does the Bible say that God did it? If yes: Is God able to do it? Then the answer is always a resounding yes.
We are not almighty like God, and so, I can appreciate that it can be difficult to take miracles at face value. But let me give you an illustration:
If you write a novel, how easy is it for you as the author to pen down a miracle in the story? Will the characters in the book object if you, out of your own creative imagination, make a donkey speak? No. You as the author is not bound by the internal rules and logic of the book you're writing. You are free to write anything you like. Then is not God, who is not a mere author of a book, but the author of the entire universe and everything therein, much more able to produce a miracle? He most certainly is.
It makes no sense to cherry-pick which miracles in Scriptures we should believe in and which we shouldn't, for they are either all true or all false. To be sure, they are all true. A donkey spoke, Christ was born of a virgin, and He died and was raised to life for us. How a miracle works scientifically is not important. For example, when Christ walked on water - did He become light? Did the water become hard? It's irrelevant and unfruitful speculation, for it's simply not a hindrance to God. Instead of asking HOW a miracle occurs, it's much more profitable to ask WHY it occurs. What is God showing or telling us through the miracle? John tells us. They are signs given to us that we may believe that Jesus is the Christ, the Son of God, and that by believing we may have life in His name.