The file that you downloaded is only a script for SIP phones. It doesn't contain the SIP binary file.
You need to download the large (53MB) zip file with all of the Avaya VOIP software at:
Specifically, download the file 46xxH323_030909.zip which contains both h.323 and sip images for various phones.
You should also download the 46xxsettings.txt file:
ftp://ftp.avaya.com/incoming/Up1cku9/tsoweb/9600/051209/46xxsettings.txt
Upgrade instructions are found at:
ftp://ftp.avaya.com/incoming/Up1cku9/tsoweb/ip_telephone/030909/4602_10_20_readme_SIP_R2_2_2.txt
Before you try the procedure below to load SIP, you need to upgrade the phone to the H.323 code, version 2.3 or later. The large zip file has version 2.9 in it. The 46xxupgrade.scr will direct the phone to upgrade the H.323 code when it loads. So, you need to put this software on your tftp server. If you don't have one, there are several you can download on the Internet, or you can use the app available for download on the Avaya website:
ftp://ftp.avaya.com/incoming/Up1cku9/tsoweb/iptel_avaya_tftp.exe
But, to provide a step-by-step summary:
1) Download the zip file and unzip the files to your tftp server directory. Also make sure the 46xxsettings.txt file and 46xxupgrade.scr files are in the tftp directory
2) Boot up your phone. When it says 'Press * to Program', press the * key
3) Press the # key for each item the phone presents, in order to skip through them. Keep pressing # for each message, until you get to 'Enter Command'
4) Press the Mute key and then 73738 (spells RESET) and then #
5) Press # for Yes, each time it asks. This will set the phone to factory values.
6) Let the phone reboot. When prompted to press * to program, press *
7) Enter the pertinent information (ip address, subnet mask, gateway, call manager (your freepbx), file server (your tftp server). Press # to save the values.
8) Keep pressing # until you get to 'Enter Command'
8) Press the Mute key and then 755 (spells SIG) and then #
9) Press the * key to change the SIG value to SIP, then press #
STEP 9 IS THE KEY STEP TO GET THE PHONE CONVERTED TO USE SIP
10) The phone will reboot, and should then find the tftp server, load the 46xxupgrade.scr file, and then load the SIP binary via tftp. It will save the binary to flash and then reboot again.
11) After it saves the SIP binary to flash and reboots, it will load the 46xxupgrade.scr, 46xxsettings.txt file, and should then get to the point where it asks for an extension. Give it the extension you created in freepbx.
Hope this helps. I believe that it covers all of the steps. My IP PBX (PBX In a Flash) is not currently running, so I'm pulling this all out of memory.
RonB