Then I tried to install the itrans53 program
but I only got error messages.
The problem may be that things have changed considerably since Jaguar and itrans53 might need a lot of fixing to work with what is now in OS X.
I would still be curious to know what, if any, the shortcomings of the online version are for your work.
Other then that I am in search for the best fonts
and easiest to use.
There is only one OS X font for Unicode Devanagari, Devanagari MT. Windows fonts cannot be used for correct display. If you are going to work in a non-Unicode format, like XDVNG, you may be able to find more options with a Google search.
For IAST Latin transliteration, there are a lot of fonts with the necessary characters. One that was especially aimed at this , I think, is Gandhari Unicode:
http://andrewglass.org/fonts.php
However, if you are working in a non-Unicode format, then you will need one of the CX+ fonts.
If the final output of your work is designed to be put on the Internet or electronic distribution (rather than printed), I would strongly recommend you use the Unicode stuff, as it eliminates the need for readers to install special fonts.