It is possible to install a local only copy of FFmpeg and direct the ./configure process of an application to find this specific copy by manipulating the PKG_CONFIG_PATH variable. An example here:

https://help.ubuntu.com/community/CompileVLC#FFmpeg...

which shows the local copy and for vlc the ./configure process is altered to include:

Code:
PKG_CONFIG_PATH="$HOME/vlc_build/vlcdeps/usr/lib/pkgconfig" \
Once this is scripted it is not so painful . Hopefully something similar will work for kdenlive...