Yeah, no worries. I hadn't noticed any problems with the sound quality so I was surprised that you felt there were so many issues. Even on something as basic as sound quality there are still very diverse opinions. I find that fascinating.
"Angel of Doom" does feel much thinner and more transparent. I think part of that is arrangement / orchestration which isn't as dense as "In My Spirit". It does thicken up a little during the last minute or so, but to me it still sounds comparable in terms of sound quality to "In My Spirit". I suppose maybe just a slightly better mix, but it is easier to get a good mix with less sound and there's a lot of volume and activity throughout "In My Spirit".
You're right about the bell. When the choir comes in it does get buried. I can still hear it though and it's more of a supporting element. This is just pure speculation, but based on its timbre and role, I would assume that the only way to keep it prominent in the mix would be to crank the volume during mixing. To me that wouldn't make much sense as by the time the choir comes in, our focus should be on the choir supported by the strings and trumpet. At that point the bell is just fluff for the overall soundscape. That's just my perception though. Maybe it should be a little clearer and they did mess up.
I'll pay more attention to the piano tracks the next time I listen to the soundtrack and see if I notice anything new.
EDIT: On a random side note, I noticed you own many of the Evangelion CDs. Are you a fan of Sagisu or just the Evangelion franchise? I ask because I don't know many people who are fans of Sagisu, but I just love his stuff. I don't know exactly what it is, but he just resonates with me. There's something about his music that's very simple and efficient while still being highly effective in context and worthwhile to listen to.