Problem with notes being shifted when copying from one piece to another

The notes are actually correct in the second score. Check the clef, which is the octave-transposing clef commonly used for guitar. All notes in this staff sound an octave lower than written. That's because the guitar itself sounds an octave lower than written. The low "E" on a guitar is octave almost two octaves below middle C, even though it is written only a few ledger ledgers lines below the staff. And the high "E" string for guitar is only just barely above miuddle C, even though it is written on the top space of the staff.

So the line you have written is actually extremely high on the guitar. The "C#" you are starting with, for example, is very high up the neck on the highest string. Also, you are using the "Steel String Guitar" sound according to the mixer. Presumably you'd like one of the other sounds better, like the Nylon String Guitar. But it will still sound quite thn because those are extremely high notes on the guitar.