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[1]
So basically you're saying that given

\emph{ alpha }

where alpha is any arbitrary string of characters (including newlines), you wish to replace it with

alpha

correct?

[2]
Do you...

$ awk '/fasta$/{split($NF,m,".");printf m[1]}/SCORE/{printf " %s\n",$4}' the_file

100 0.6043
101 0.8360
103 0.8705




Please use code tags, thank you

I ran that:
$ awk '/fasta$/{split($NF,m,".");printf m[1]}/SCORE/{printf " %s\n",$3}' the_file

100 4.145
101 2.665
103 3.665

I just tested using GNU gawk, and it worked for me.
awk -f awk_parser.awk the_file

I'm new to this forum and editor, so it may not tab-align properly, but this worked for me:
BEGIN {

...