Hi.
I suggest that you will try the following before paying for script modification:
1. make sure that the server does support long PHP script execution (so it won't die in the middle)
2. add a log to see the status
PHP by definition is not supposed to do long runs, but it can. you just need to make sure you don't exceed it's boundaries - but if you do, just change the boundaries :)
If that doesn't help. and your script is running well. I assume that you just need to create a queue from the file and then running on the queue in bulks.
Cheers,
Ika