Can I use AppleScript to paste a web text clip appended with source attribution and a timestamp, while maintaining embedded links?
I'm a bit confused by your script, it seems to copy and paste and delete and save, so if I misunderstood your intended use, I apologize. It seems to me like you want a file saved in that Web Clips folder that just contains what you had selected in Safari with the link, title, and date. I would write this as an HTM file rather than a text file, and here's the code I used with inline comments.

set myFolder to ((path to users folder) as text) &amp; "Web:Documents:Web Text Clips:"
set myFile to myFolder &amp; "Web_Text_Clips.htm"

tell application "Safari"
set theLongDate to current date
set theWindowName to the name of the front window
set selectedText to (do JavaScript "(''+getSelection())" in document 1) --use javascript to get what part of the page is selected
set theURL to the URL of the front document
end tell

set myFolder to POSIX path of (myFolder as alias) --convert to posix path for use in the command line
set myFile to quoted form of (myFolder &amp; myFile) --append the file name to the end of the file path
do shell script "touch " &amp; myFile --create the htm file

--Add content to the HTM document
newHTM(myFile) --Add the HTM doctype and opening tags.
addElement("p", "--------", myFile) --"p" is the htm tag for a paragraph, and we want this to be it's own paragraph. 
addElement("p", "From: &lt;a href=" &amp; theURL &amp; "&gt;" &amp; theURL &amp; "&lt;/a&gt;", myFile) --a bit more complex, adding a paragraph with a link (&lt;a&gt; is the link tag)
addElement("p", "Page Title: " &amp; theWindowName, myFile) --Adding a paragraph for the Page Title
addElement("p", "Date: " &amp; theLongDate, myFile) --Adding a paragraph for the Date line.
closeHTM(myFile) --Add the closing HTML tags.

------------HANDLERS------------
on newHTM(filePath)
    do shell script "printf '&lt;!doctype html&gt;\n&lt;html lang=\"en\"&gt;\n&lt;head&gt;\n\t&lt;title&gt;Web Clips&lt;/title&gt;\n\n&lt;/head&gt;\n\n&lt;body&gt;\n\t' &gt; " &amp; filePath
end newHTM

on closeHTM(filePath)
    do shell script "printf '\n\t&lt;/body&gt;\n&lt;/html&gt;' &gt;&gt; " &amp; filePath
end closeHTM

on addElement(elem, htm, filePath)
    set htm to "\t\t&lt;" &amp; elem &amp; "&gt;" &amp; htm &amp; "&lt;/" &amp; elem &amp; "&gt;\n"
    do shell script "printf '" &amp; htm &amp; "' &gt;&gt; " &amp; filePath
end addElement


This script preserves the link by using HTML to "embed" the link. It will open in your default browser. It appeared to me, from your script, that this file only contains the latest web clipping, so that's how I wrote it. If, however, you want this file to contain a list of web clippings, the script would need to be edited. Either way, I hope this gives you a good start. For readability, I put the adding of html code in handlers below the body of the code.