Michel, your work is close to that of Ulrich and it's interesting. Based on his findings I collected https://www.dropbox.com/s/0k3uuodvksltjxq/Stiehl2007-color.pdf
For some ligatures like sla with Siddhanta you show 2 variants, but visually I can't find a difference. What do you mean by them? Or there was a difference in the books you quote, but none in Mihas font?
How did you tel TeX to show different ligatures of the same sounds? I'm not familiar with Unix-like Nagari fonts, is there an .ttf or .otf file which can be downloaded to reproduce the same on my PC? .pdf is good for looking, but bad for working with it further. I'm working on compiling a list for a Sanskrit Reader. I made a concordance based on 14 Sanskrit Grammar's and it shows more than 1046 yours and more than 807 Ulrich's. As Ulrich's algorithm is not open source, one will have to do it once again, to check his words.

The file above is part of the documentation that comes with the LaTeX Sanskrit package. For the full documentation, see the file sktdoc.pdf of the link above that should answer your questions.

That table had been referred to by John Hudson 4 Sep 2012 — 6:45pm in the thread Adobe Devanagari Font that Uli Stiehl had started in Aug 2012. I should have added a back reference, http://www.typophile.com/node/95460?page=1#comment-521244 to provide the context. The table was put here for technical reasons.

*Edited the back link to add the page number for it to work.

is there an .ttf or .otf file which can be downloaded to reproduce the same on my PC?

Not that I know of. The LaTeX package skt.sty uses Type 1 PostScript fonts.

skt8.pfb     PS Type 1 font file for skt font at 8pt upright.
skt9.pfb     PS Type 1 font file for skt font at 9pt upright.
skt10.pfb    PS Type 1 font file for skt font at 10pt upright.
sktb10.pfb   PS Type 1 font file for skt font at 10pt upright bold.
sktf10.pfb   PS Type 1 font file for skt font at 10pt upright feint.
skts10.pfb   PS Type 1 font file for skt font at 10pt slanted.
sktbs10.pfb  PS Type 1 font file for skt font at 10pt bold slanted.
sktfs10.pfb  PS Type 1 font file for skt font at 10pt feint slanted.

(the list above is a copy-paste from the README file).

For instance the file skt10.pfb, Wikner Sanskrit 10pt Upright, contains 222 glyphs that, put together, can give a nice looking pdf output. To put those 222 pieces together in order to produce a final Sanskrit text from an ASCII input file, a preprocessor whose source is contained in the file skt.c (coming with the texlive 2012 distribution) needs to be used.