#1
I'd say I have a pretty good ear for music and I can hear when things are wrong/ out of key.

The thing is, this doesn't translate as much for my guitar. What I've noticed is that when I hear a note and I go to play it on the guitar, I'm usually a whole tone lower than the actual note. It's usually always like this. I should probably just always make a conscious decision to play two frets higher than I normally do

Is this just bad note visulisation or is it normal?
Breakfast, Breakfast, it's great for us
We eat, we eat, we eat
That frozen meat
Oh boy, oh boy, oh boy, it can't be beat
#2
Story of my life. Happens to me all the time.

I know this post doesn't help much but I feel better now seeing that I'm not the only person who has problems with intonation.
#3
Ah, so it's intonation.
I read that as being guitar intonation at first
Imagine my intonation being so bad that my guitar is 2 semitones flat

It's not that bad really, I still consider myself a good improviser and composer. I sometimes find out very interesting chords and melodies when I mess up with note recognition.
Breakfast, Breakfast, it's great for us
We eat, we eat, we eat
That frozen meat
Oh boy, oh boy, oh boy, it can't be beat
#4
you're not alone, the guitar is a very hollow (no pun intended) instrument by itself. when you play a single note on a piano versus a guitar, it's infinitely easier to recognize notes. but you'll master it in time. people who have been playing music for decades still don't truly master their instruments, don't sweat it bro