At that point I started to consider that perhaps this was not his story. But I was not going to give up that easy. I did not want to give up on him so easy because to me he was far more than just another character. Parts of me are in him and he is very loosely based on someone that I admire a lot and has been inspiring me for a decade. I did more research in the hope to find something that would enable me to bypass his problem and make him fit in the story nonetheless. The answers I found were not the ones I wanted. Maybe this was not meant to be.
I was very close to killing him. I did not want to and the thought alone made me very sad, but it he would probably cause the whole story to come crashing down and I wanted to avoid that at all costs. I ensured myself if I had to kill him, I would not bury him. When the time was right, I would resurrect him and give him his own story. But luckily I did found a solution. A very simple one, actually. The trauma of his past was not important for the story, so why would I make him suffer so much? Taking the trauma away wouldn't fundamentally change him but it would make him able to be in the story. Everything is now starting to fit together again and I am very relieved because of this.
But finding a solution for one character/scene/plot point/sentence/... does not mean there will always be a way to make it fit. You always have to look at the bigger picture. If something does not fit in, do not force it. It will make your story's quality go down. It is not because you kill it now, that you cannot use it later. Keep a notebook or a document were you save all the ideas and things that had to go because it did not fit. Maybe in time you find a way to rehabilitate them. Writing is great fun, but sometimes I can be very hard and it can even suck. Turn your heart into a stone and kill everything that does not fit.
"Kill your darlings, kill your darlings, even when it breaks your egocentric little scribbler's heart, kill your darlings."
On Writing by Stephen King