This is how I would do it:
1. Since poison is a save or die effect, do most folks here think it's okay for the Assassin to be able to buy poisons or think they should make it themselves?
Buy it on illegal places and risk prison or worse.
2. GMs, do you put any sorts of limits on the Assassination ability? Can any monster literally be Assassinated for example?
No restrictions on humanoids, for other creatures I might ask for some previous anatomy knowledge and could give a ST bonus if seems right for the creature's anatomy. (I take assassination as a strike on a vital point, something that the assassin must be aware of and the victim must have).
Also the supplement lists not granting a monster who is 2 levels or more lower than the Assassin a saving throw. Do most follow this optional idea?
I would't follow it, I like the chance of failure.
3. In earlier editions the Assassin had to achieve surprise in order to Assassinate something. In this version it looks like the Assassin follows the same protocols as a thief backstabbing where surprise isn't necessary. How have others played this?
Same as in Backstabb, but I would add a -2 surprise penalty on the ST.