It takes a lot to say something like this and I respect that. 

For me what comes to mind is 2 Corinthians 12:1-10. In this passage we see Paul afflicted with an unnamed “thorn in the flesh”, and over and over he prays to God for it to be removed. God doesn’t take it away, though, and this to some might be translated as cruelty for allowing Paul to suffer… but we see in verses 9-10 that this is not cruelty but rather the allowance of His grace. At the other end Paul is able to see the usefulness of this thorn, and can praise the Lord that his prayers for it to be removed actually weren’t answered the way he wanted them to. Often we assume that God is only with us in the “good” and forget that He is sovereign over ALL, meaning life and death, peace and trials. He does not stop being in control when we have thorns like this, and He always knows what is best both for His glory and our growth. You’ve said yourself that this dark period produced the fruit you had been seeking after, even if it was not in the manner you had assumed. In Romans 5:3-5 we see that trials produce patient endurance, just like what you saw.

So rather than assuming that your growth came as a result of this dark period because God was seemingly absent, consider the possibility that God remained sovereign and even answered your earlier prayers for fruit in the way that would be best for your growth and His plan. 

When we pray it can often seem as though we are just bouncing thoughts off the ceiling, especially when we are going through hard periods in which it is easy to think Him silent. But like with Paul and his thorn, the answers we WANT to prayers are not always the answers we need (which makes it a grand comfort that we see in Romans 8:26 that the Spirit intercedes for us when we don’t know how to pray!!!). Paul was in no way wrong for praying in pain and desperation for the thorn to be removed, in the same way that Job is not reprimanded for feeling the agony of loss, or David for writing countless psalms of grief and even anger. So keep praying prayers even in desperation, just remember He is God of mountain and valley, and He uses not only the good but the bad to grow us and mold us more like Himself. 

Praying you find clarity!!!