Can I drag this back to the original question? Thomas mentioned that Adobe's EULA allows modifying fonts for internal use, and many of us are very grateful for how Adobe stands out in this regard. (In the 5-seat EULA, the relevant paragraph seems to be no. 14.7.4.) However, the OP speaks of preparing material for "propagating" Sanskrit, which doesn't sound like "internal use." On the other hand, the very next paragraph (14.7.5) speaks of embedding, which is allowed for printing and viewing, and would seem to provide an avenue for propagating documents with custom Sanskrit diacritics.
In other words, is it permissible to embed a modified Adobe font in a PDF that is used to print a document that is then distributed on paper? Is it permissible to make such a PDF available for downloading? Of course, much of the value of a PDF is that the information it contains can be indexed and searched electronically, and under those circumstances it is far better to render macron-a with the appropriate Unicode encoding, rather than by kerning the macron character over a bare "a."
I rather expect Adobe would prefer not to be more specific, and risk opening up a can of worms here--as Thomas says, a contract is a contract. But I also expect Adobe would not go after those who strive to uphold the spirit of the contract (as well as the design qualities of the original typeface). I hope I'm not way off base.
Thanks,
David