Well I was able to fix the above  issue by:
./configure --with-ffmpeg=/usr/local/cpffmpeg
Then looked at phpinfo and sure enough ffmpeg php module is now active. But now everytime a script calls for it, The Apache error log file spits out all this garbage now and no video converting 

[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40] ffmpeg version 0.9.1-syslint, Copyright (c) 2000-2012 the FFmpeg developers, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   built on Nov  1 2015 16:42:55 with gcc 4.4.7 20120313 (Red Hat 4.4.7-16), referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   configuration: --prefix=/usr/local/cpffmpeg --enable-shared --enable-nonfree --enable-gpl --enable-pthreads --enable-libopencore-amrnb --enable-decoder=liba52 --enable-libopencore-amrwb --enable-libfaac --enable-libmp3lame --enable-libtheora --enable-libvorbis --enable-libx264 --enable-libxvid --extra-cflags=-I/usr/local/cpffmpeg/include/ --extra-ldflags=-L/usr/local/cpffmpeg/lib --enable-version3 --extra-version=syslint, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   libavutil    51. 32. 0 / 51. 32. 0, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   libavcodec   53. 42. 4 / 53. 42. 4, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   libavformat  53. 24. 2 / 53. 24. 2, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   libavdevice  53.  4. 0 / 53.  4. 0, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   libavfilter   2. 53. 0 /  2. 53. 0, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   libswscale    2.  1. 0 /  2.  1. 0, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   libpostproc  51.  2. 0 / 51.  2. 0, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40] , referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40] Seems stream 0 codec frame rate differs from container frame rate: 1000.00 (1000/1) -> 25.00 (25/1), referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40] Input #0, flv, from '/home/radioga/public_html/vidi/uploads/small.flv':, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]   Metadata:, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]     audiodelay      : 0, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]     audiosize       : 25162, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]     videosize       : 589575, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]     hasCuePoints    : false, referer: 
http://radiogaga.ga/vidi/upload[Thu May 26 13:44:25 2016] [error] [client 24.139.25.40]     metadatacreator : inlet media FLVTool2 v1.0.6 - 
http://www.inlet-media.de/flvtool2, referer: 
http://radiogaga.ga/vidi/uploadAnd more and more of that.......