Best way to farm the stalker is this:
- Run any boss run aside from Tolstoj (Vor). I usually run Tethys on Saturn.
- Run M Prime on Mercury. Just speedrun it and don't care about any enemies, just grab the objective and run back.
- As soon as the stalker appears and after you've killed him, do a bossrun again.
- Do M Prime once again until Stalker appears.
This really is the best way to farm for only the stalker. Then again, just doing any boss run and running any mission you want is just as good, although I'm not sure if he can appear in any Assassination missions (he can appear in void maps, had this before!). It's just that you have to be 'flagged' once by killing a boss and then any mission has the same % of chance for him to appear, although M Prime is definitely the fastest. Speed it up a bit with speedhacking on 2-3 times and you're good to go.