Bleh, Just contacted the host, and there is no access to PHP from the command line, so that pretty much eliminates that idea.
The only thing he suggested was a program called MySQL-Front, which is more for managing a database with a pretty front end.
I have split the files up into even smaller files now, anywhere from 14MB-19MB in size. And after reading each file, just give the user a button to press to go on to the next file. Its a little half assed but it may just work. Either the button or have javascript forward them onto the next page passing the file number as a variable in $_GET.
After running it as stated above with javascript, it still seems to timeout after the third file.
