I had the exact same problem: I couldn't get Youtube notifications to work the way I wanted.

I can't help much on the "new comment" notification front, but I do have an alternative solution for receiving "new upload" notifications. I was so frustrated that I added Youtube to Zapier myself.

I have a Zap set up that sends me an SMS whenever a video is uploaded to a certain channel. You could use this Zap to send you an email notification for new uploads.

UPDATE I can't guarantee this works.. Google keeps changing things. e.g. March 2016 google changed my settings to spam me, and i've suddenly started receiving email about comments that have nothing to do with me. The emails can be turned off (there's an unsubscribe link at the end of each email), but will update about notifications.

There seem to be two places where notifications are, this one seems to work, it's the google+ notifications https://plus.google.com/u/0/settings

and there's also this one which may work too
https://www.youtube.com/account_notifications

But I fixed it by going to the google+ notifications link mentioned, i.e. https://plus.google.com/u/0/settings

To get to the Google+ notifications page you can also go to the bell in the top right

this is what the bell looks like on youtube.com

this is what the bell looks like on support.google.com

I am going from youtube.com

Now

Expand the bell and click "google+ notifications"

A bar like window then appears on the far left.

Now click Settings at the bottom of there

And you should hopefully be able to get this page

now looking at that page above, then scroll down expand "Posts" as in the pic below, and you see the pic below, these checkboxes, and notice I have deselected two of the options, this cuts down on a lot of the junk. So, if somebody refers to me then fine, I get a notification. But I change two of the defaults, because if somebody just replies to a comment I made, I don't want a notification 'cos lots of people might reply to a comment. And if I participate in a comment thread I don't want to be notified forever after every time somebody comments. These are stupid defaults that I have changed, deselecting them.