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Well, if you read the Quran, it says regarding mountains that we inserted them into the earth like nails. And, if you read the geology of mountains, it says the same. That is to say that these are not only taller in heights but also deeper inside the earth too. If you read and compare nature of things with the divine knowledge you will learn a lot. 

It's because you are overthinking brother. In my opinion, doubt is very different from waswasa (evil thoughts from shaitan). Doubt is when one thinks like: Rasool (صلى الله عليه وآله وسلم) did that?? I think he must be a false Prophet etc. these things are considered as doubt and those verses and hadiths you mention, address this. That it's hypocrisy and disbelief. in your case, it's evil thoughts (waswasa) coming to you by shaitan with no basis which you want to get rid of, i:e you get scared you turn to Allah because you can't even think of committing kufar or following those voices. Faith isn't something magic you see, it's not something tangible you need to relax and tell your mind whatever the thoughts are, i'm gonna ignore as i am a believer. Period. Also, distract yourself with work/games surround yourself with people avoid being alone. sometimes it happens being alone makes us overthink alot. As for genuine questions that come to your mind, be brave and find the answer. Post here we'd be happy to help if we can. Religion isn't something you've to believe in blindly. Question each and everything and keep looking for the right path. God will never punish those, who were genuinely researching and looking for his path but couldn't due to death or their mind couldn't comprehend it. Take it easy. everyone will be question w.r.t aql he/she have been blessed with.

Considering i spent most of my time indoor with little social life and dislike for outside... Well i do like mountains, and i did see mountain in the past, i love them, and i was in awe. But there was little to no spark. Usually religious people go there, they immideatly go "what a magnificent creation from God" meanwhile I didnt think any of that, to focused on my daydream and just staring at it. I have to think for a bit before going yeah I guess ill say MashaAllah, but it feels forced Which keeps reinforcing the belief that deep inside my heart isnt believing or something, God i hope not

But even when the doubt is gone, point 1 to 6 stays. These last few days my prsyer has been horrendeus

It has been found that the work of Naimatullah Shah Wali has been adulterated with fabricated material. So, it would be wise not to show too much interest in that.