Hi Michael, Here is a partial response to your queries:
1. The language has two notations/spellings, an old one and a new one (since 1978). Do we just look at the new one?
It would be useful to document both, but the for the root zone LGR, the Procedure requires "being used for everyday writing": "...Any character that cannot be authoritatively established as being used for everyday writing in a living language will be excluded. ... it is the responsibility of a generation panel to come to a definite conclusion whether it is both safe and useful to select a particular code point as candidate for the repertoire. In case of uncertainty or doubt about the expertise or the authoritativeness of the information available, the panel must exclude the character as candidate." (see https://www.icann.org/en/system/files/files/draft-lgr-procedure-20mar13-en.p df, pg. 30) It is up to the GP members to decide if the older system still qualifies this definition, and in that case also provide authoritative references to support it.
2. I found a letter that is actually a combination of two letters ("ny"). Since the language has both "n" and "y", I would think, we just ignore this. Or do we have to keep track of this for later variant rules?
Again, it would be useful to keep a note of it until the variant analysis is done. It may be hard to predict at this time how this may or may not be relevant until the GP has discussed how it defines variants (if any) for Latin script. Regards, Sarmad