The Gr"a says each seder in mishnayos and gemara, has it's own type of influence on a jew's avodas H-shem.
Zeraim for example, which is the first one, "plants" the seeds of emunah and ratzon to fulfill the will of H-shem.
And from there, each seder adds and builds upon the ones which preceded it, until Taharos. Which is the highest level of avodah.
So if your thinking about how to counter tumah with mishnayos, the answer would probably be to start from Berachos and work your way through gradually. Build yourself over completely, in the correct order. What could be a better way of purifying your mind?
(The following is only my opinion, I think chazara is more important that the original limud.)
Beracha v'hatzlacha to anyone who ventures out on the journey through shas. Rememeber - time flies, so even if you only do one mishnah a day, you've been through over 50% of shas in 4 yrs.

I think this is a really good idea - thanks kedusha! I would say that its depends on whats driving you at the time. I find that bound together with my lust is an emotional fascination with women in general and learning nashim is a way of channeling that drive positively. The graphic gemorrahs can be trigering in a weak moment though so I think one has to be honest about how they are doing at that moment before learning those sugyas.