Applescript for multiple find/replace using separate masterlist
You must use the text from the first document instead of putting it into a list.

Put the searching text and replacing text from the second document into a list.

Like this script :

tell application "Finder"
    set filePath to (first file of folder "Data1" of desktop) as alias
    set filePath2 to (first file of folder "Data2" of desktop) as alias
end tell
-- get unique text from the first column
set uniqueText to do shell script "awk -F'" &amp; tab &amp; "' 'BEGIN{getline}{print $1}' " &amp; quoted form of POSIX path of filePath

-- get unique text from the first column, but print the first and the second column to get the searching text and the replacing text (pair), this put the awk's result into a list
set uniqueList2 to paragraphs of (do shell script " awk -F'" &amp; tab &amp; "' 'BEGIN{getline}{print $1\"\\t\"$2}' " &amp; quoted form of POSIX path of filePath2)

set uniqueList to my replace_chars(uniqueText, uniqueList2) -- find/replace data, put the paragraphs into a list

to replace_chars(t, L2)
    set tid to text item delimiters
    set tc to count L2
    repeat with i from 1 to tc
        set text item delimiters to tab
        set {toFind, toReplace} to text items of (item i of L2) -- get items separated by tab from a item in uniqueList2)
        set text item delimiters to toFind
        set {L, text item delimiters} to {text items of t, toReplace}
        set t to L as text
    end repeat
    set text item delimiters to tid
    return paragraphs of t
end replace_chars