Your description of what you want done and your statement of what should be in File3.txt don't match. If you don't give us a clear description and example of what you want done, we can only waste time guessing at what you want to do.
For the sample input you provided and the sample output you say you want, the simple solution is the following command:
cp File1.txt File3.txt
A simple way to do what you said you wanted done (ignoring the samples your provided) would be something like:
awk -F "|" '
FNR == NR {f[$1] = $0;next}
$1 in f {print f[$1]}' File1.txt File2.txt > File3.txt