I have a feeling that 'Tears for a father' and 'The boy - A day away' somehow belong together. The boy in real-life tells a story about (school and) stealing apples while a simular situation happens in the beginning of 'The boy'..... so, maybe he can hear 'his son' and that little story brings him back to his own childhood (in his dreams!) where he himself played with a friend.
Yeah, I think so too. The son at his hospital bed tells him about that thing with the apples from the tree and as soon as he leaves and turns on the radio, our patient remembers several childhood memories, too. He re-lives some adventurous things from his childhood.
maybe a long shot here but: is he her son whom she lost a long time ago? Is it his name she was crying out?
(...)
I'm not sure here but i guess that he had been left behind by his mother and her new man. The mother always deeply regretted her decision but now, after all these years, they have found each other again. Our patient feels strengthened by his discovery and is ready to get out of his coma.
That's one way to see it, yes. The guilt of leaving his mother behind kept him trapped inside his head. In "Paradise" he sings
"I smell their little lies, FATHER!!" which could mean that he knew about the mother cheating the father in real life and he turned his back on his mother and the new man - OR it could mean that his father turned his back on the mother (
"turn away, baby, forever I'm gone")!
Another way to see it is that this woman who's crying out is his wife whom he neglected a lot in real life so that she was so desperate for love that she cheated on him - which is when the son was conceived. This seems to be the content of the first lines in "Break The Silence" (from 0:00 to 1:25):
"I think about love and the things that I've done,
A heart open wide and I stabbed a knife.
How could I feel the way that I've felt
I felt it was love, and was heaven-sent.
You set me free, never cared for me.
I needed love, a touch from your hand
I need to feel you care.
Then there he was, made me feel whole inside,
this burden of guilt tears me up
You must believe...
I'VE TRIED!!!"
She really tried staying true to him but he didn't show her that he cared at all, so when that other man came and made her feel whole inside, she just
couldn't take it anylonger and betrayed him with that man.
I'm trying to interpret some lines from "Hide & Seek" all the time but it's really difficult because there are different things one can interpret into those lines!
For example:
"I can feel her pain running through my veins"
This could be his
mother's pain he feels - but also his
wife's pain while she's living her life without him, waiting for him to wake up from the coma. So what exactly does the woman in Mercy Falls in his head embody...? Dammit...
"I can sense the joy from this little boy, the hole in my soul starts to heal"
I can imagine that this is his his son (which isn't really
his son, you know what I mean). First - in "Break The Silence" - he neglects him quite a bit because of the fact that it's not
his son (
"this lazy boy can help" and
"thanks for the help, here's a dime, now off you go").
But after a while he seems to accept this fact and begins to accept him as a son and as soon as that happens, his 'wounds' start to heal.
So my final thought is:
As soon as he's finally ready to accept his son as
his son and also experiences the pain from his mother, he decides to reunite with his mother who's been in such pain and loneliness without him. And as soon as he experienced the desperation of his wife, he decides to care more about his wife, whether or not she cheated on him, he decides that he has to wake up, but for some reason he can't. We then find out that the doctors think he doesn't wake up because the bone marrow transplant didn't help - they don't know that it was just his head, his psyche that kept him from waking up - so after the doctors say that there's no more hope, his wife decides to pull the plug.
In "The Black Parade" it says:
"Hold on tight and never let go, don't let go"
If he hadn't neglected his wife, but instead lived with more passion and care she wouldn't have cheated on him.
And I think that the part
"Hard to see behind a wall of darkness" means that he was shocked about the boy not being his son but after he felt the love and care and joy from that boy, he knew not to care about such (almost superficial) circumstances but simply see the boy as a boy and not as someone who doesn't belong to him.
"Cause when time runs out, all your fears will be inane" means that life's just too short to neglect people, to abandon people, to be angry at people and to not care about people. Also it may be a warning like: the man has been in the coma for so long that now time has run out. If he had overcome the walls inside his head, he would have had the chance to wake up before anyone pulls the plug!
And I'm afraid I must have misunderstood quite a lot, haven't I...?
, my compliments to the band! 
