Thanks to KenS hints I was able to solve my problem. The encoding used wrong character names like kafinitialarabic (i mean by wrong, pdf could not understand that), everything that ended with arabic was wrong. The Traditional Arabic font does not have those names for characters. In order to know what it really understood, have converted the ttf font to afm and pfa using the following command, that is converting the true type font to type 42 font which will be understood once embed in postscript file at conversion to pdf
C:\Program Files\gs\gs9.10\bin>gswin64c.exe -dNODISPLAY -q -- ttf2pf.ps times tim
esPS timesAFM
where times is the ttf font name. I then checked the generated pfa file for the characters I wanted to add, instead of kafinitialarabic, there was kafinitial, and for kafmedialarabic there was kafmedial and so on...
It works fine now to add those in encoding, but I want to find a way instead of adding all those characters in the dictionary, I want to use the font like we use with setfont in postscript normally - if that is possible...