It's admirable that you're willing to work at this on your own. Teaching yourself is a lot of work. But then, so is learning the instrument even with help from others, like say, a friend, music instructor or guitar teacher.
1). Bass guitar and guitar have the same note names. Bass is just an octave lower. And then there's the obvious. . . bass only has 4 strings, usually. Yeah there are 5 and 6 string basses. Even 7 or more. But generally a bass will have 4. So if you play a note on the 6th string of your guitar, say you play 3rd fret on the 6th string . . . that's a G. On bass, you play the 3rd fret on the 4th string, and it's also a G, an octave lower than on the guitar. Both notes are technically in the bass clef. If you have standard guitar music, it will only have a treble clef, but will include (when needed) 3 additional ledger lines below the staff, and 4 spaces. But those lower spaces and lines are indeed bass clef. The G you played on guitar will be in the 3rd space below the staff.
2). You said in your explanation " the second fret- A string, the natural note is E1" I'm thinking that's a typo because later you say "7th fret on E string is the same B note". Both are B notes.
There are MANY of each note on the guitar, 3 B's in the 1st 4 frets alone. There are 2 or 3 of each note just in the 1st 4 frets. The sheet music let's you know which one to play. For example, E. 4th space below the staff, you play the open E 6th string. First line on the staff is E, 2nd fret on the D 4th string. Top space on the staff, you play either the 5th fret of the 2nd string, or play the open E 1st string. If you're using the correct fingering for open scales and open chords, you would play the open E 1st string. Playing the E on the 5th fret of the B string will pull your hand out of position.
As in, fingers 1, 2, 3 & 4 play frets 1, 2, 3 & 4. (open position) Because of how the guitar is tuned, a note on the 3rd line, B, could be played on the 4th fret of the G string, 4th finger, or played on the open 2nd string. Unless your guitar has very light gauged strings, with a plain, unwound 3rd string, you'll hear an appreciable difference between the 2 B notes. Both are B, but one is played on a thicker, wound G string, and one on a thinner, unwound string.
When reading music, you'll find pretty much it's all about the 1st 4 frets. You can play 2+ octaves on just the 1st 4 frets. And treble clef sheet music covers only 2+ octaves. As you advance, you'll begin to note when the music indicates you should be playing what's written an octave higher than written.
Something else to know ... Middle C on piano is . . . middle C. On guitar, middle C is the 1st fret on the 2nd , B string. But the music is written with middle C being on the 1st line below the staff, and for guitar, you play it an octave below what's written. So you play the written middle C on the 3rd fret of the 5th, A string. If you played the written middle C on the 1st fret of the B string, you'd end up trying to play all the notes of a song on the B and high E string, and be playing the notes horizontally as you go higher, instead of vertically, as intended. Try playing a full song's melody on just one string.
So you could indeed play something as written, and play it higher than the 1st 4 frets. But not in every key. Music below the staff for low E, F, F#, G and G# for instance, can only be played on the 6th E string. (Open, through 4th fret.) And if the melody includes those low notes, most likely the entire song will be played on the 1st 4 frets. You could, if you wanted, shift the whole song up an octave. So you actually play what's written an octave above where it's written, for all the notes in that music.
It's all about playing position. If you wanted to play a song in Bm for instance, and wanted to play it using the B on the low E string, 7th fret, you would place your fingers 1, 2, 3 and 4 at the 7th, 8th, 9th and 10th frets. Most of the notes you'll need to play the song in Bm would then be within those 4 frets.
Hope this was helpful! Best of luck. I don't know if there's a way to communicate with other members with this forum. I just joined. If there is, you're welcome to ask me questions off forum.