Applescript debugging PLEASE HELP

Question

So I wrote this automator program that basically takes a list of sequences and inputs them into a server and appends a URL on the page into a text document
It works perfectly for a couple and then randomly just stops working and it is driving me craaaazy . i've been trying different delay times but just can't seem to figure out the problem. 
so before this applescript there is a for loop then sends all the sequences to it one at a time .
1st) tabs to the text box
2nd) pastes the sequences into the text box
3rd) tabs to the Proceed button
4th) presses enter
5th) on next page, it grabs the URL that is specified at a certain position
the bug randomly happens after it pastes the sequence into the box and then it will randomly go to the URL bar at the top of Safari and get stuck doing weird things over there .  this throws off the whole flow of everything ?
I REALLY want to know why this is happening ? Why would it work for like 3 or 4 andf then act up on the next one when the format for the sequences are all the same ? Do I increase a delay at a certain position ? I think one way to bypass this problem would be to tell applescript to press the proceed link" does anyone know how to do this?
delay 1
tell application "Safari" to open location "http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi"
delay 5
tell application "System Events"
    key code 48
    key code 48
    delay 0.5
    keystroke "v" using command down
    delay 4
    key code 48
    key code 48
    key code 48
    key code 48
    key code 48
    key code 48
    key code 48
    key code 48
    key code 48
    keystroke return
end tell
delay 5
tell application "Safari"
    set thelink to do JavaScript "document.links[4].href " in document 1
end tell

Answer 1

But what about this?
do shell script "command " with administrator privileges
You can also include your password, to avoid the dialog, using the syntax:
do shell script "command " password YourPassword with administrator privileges
Though it would be kind of a security risk, its still convient...
And no, I am not the one trying to get around the block, its funny that you bring that up though, but why would I be asking how to incorprate the admin account and password into the script if I was the one trying to get around it..? But yes, thank you for your help.
Josh