1) Back then another contributor to the TZ list looked up which districts (ulusy) of Sakha (Jakutija) were in which timezone. I merely incorporated his research into my report on all Russian timezones. I tried to give him credits, but his name was somehow lost in the comments in the TZ file. I forgot, I have lost the emails, if reference is needed: please look it up yourself in the TZ mail archive. Thanks a lot for that clarification. That answers the question what your source was.
2) Transliteration scheme: back then I chose for the Chemical Abstracts transliteration which had 2 advantages: (a) two-way, (b) Posix 1 compatible. Two-way means: the transliterated text can be transformed back into Russian again. With schemes like GOST 7.79 (ISO 9) and several other schemes, only one-way transliteration is possible. http://en.wikipedia.org/wiki/ISO_9 is two way, isn't it?
3) Districts in Sakha are in this republic called ulusy (nominative case; singular: ulus), in several other Russian publications they are called rajony (singular: rajon). The law (see my point 5) gives both terms. I think "districts" is close enough for a text comment in English. http://www.garant.ru/hotlaw/federal/346568/ ัะปัั (ulus) not found on that page
4) With respect to the transliteration scheme in the comments: what are we talking about? At any rate not about any vital part of the TZ software. I wouldn't give it much more attention, if I may suggest. If you open the europe file and search for certain entities it helps they are spelled one way throughout the document. Contributors to zones using different romanizations are in a disadvantage compared to e.g. contributors to US zones.
5) The law (http://www.garant.ru/hotlaw/federal/346568/) states very clearly which Sakha districts are in which timezone. Please check this for current times in the TZ database, if not done already. Done, at various instances, earliest I found was by Alexander Krivenyshev Timeline compiled yesterday http://mm.icann.org/pipermail/tz/2012-May/017688.html
There is however one not so clear part, namely the Newsiberian Islands. From memory I recall that one TZ contributor said they are administered from the central government of the republic. Heaving read several texts and looked at a couple of Russian maps, I'm inclined to believe the islands are part of the Bulunskij Ulus. Regretfully I have no definitive reference for you. 2011-09-20 Tobias Conradi reports that the New Siberian Islands are maybe not part of the Ulus-system http://mm.icann.org/pipermail/tz/2011-September/008836.html
Then again: how many people actually live in this reserve? So, what is the effect if we put it into the wrong timezone? The database would contain a bug according to tzcode2011i/Theory:
----- Scope of the tz database ----- The tz database attempts to record the history and predicted future of all computer-based clocks that track civil time. To represent this data, the world is partitioned into regions whose clocks all agree about time stamps that occur after the somewhat-arbitrary cutoff point of the POSIX Epoch (1970-01-01 00:00:00 UTC). -- Tobias Conradi Rheinsberger Str. 18 10115 Berlin Germany http://tobiasconradi.com/