Hello, Guitar Covers! I understand what is meant by the sentence. However, the flow is a bit unnatural. If I were to re-write it a bit I would state it as follows:
I always prayed for what I have today but never anticipated the difficulties I would face when my prayers were (actually) answered.
I would include the word actually if the person did not expect the prayers to be answered in the first place.
As for whether "I always prayed" or "I have always prayed" mean the same thing. Well, not really, in my opinion. "I have always prayed" is a more general statement about prayer whereas "I always prayed" would likely be used for specific situations. For example:
I always prayed for rain during the summer drought season.
I always prayed for a safe journey when we would travel the country by car.
I always prayed that my sister would make it home safely.
Other might be an answer to a question:
Person A: I noticed you praying over there, you don't seem like the praying type...
Person B: Oh no, I have always prayed.
Person A: This is hopeless, what are we supposed to do in situations like this?
Person B: In my case, I have always prayed.
Hope that helps, to me the first is for specific things, second is more general. That is my non-English teacher but native English speaker opinion. :)