I have solved most of the problems.
By commenting out the two lines of
#RewriteRule ^ar[\/]?$ index.php?lang=ar #RewriteRule ^en[\/]?$ index.php?lang=en
And many of the problems got resolved with the following post I found just now:
Displaying content based on language with qTranslate
Biggest problem I have now is the mixed HTML texts which need to be switched in Arabic. Within the template I tried qTranslate shortcodes and the
<!--:lang--><!--:--> tags but they do not work there. Also, writing arabic directly into HTML is not a good idea I guess.