I can't help you with ioncube as I refuse to use it and therefore have no experience with it.
As for ffmpeg-php, you will need to install autoconf yourself first.
There may be a way to work-around the requirement for "root" access to install a working flvtool, but I have never tried it, so I can't help you there.
Just curious: why do you want/need these things for processing video on the webserver? It seems to me that those things are best done on your won desktop rather than using he webserver's resources for that kind of processing.