Before I say anything may I point out that this build is more for fun than anything else, and has yet to be tested in ranked gameplay.
However, for those who like to experiment with unorthodox builds, then this build may be of use to you.
The rune pages simply are trying to maximise your effectiveness in the specific roles; as much AP as possible for laning, and a little more sustain for jungling. The basic concept is, in my book, spam AP and try to grab some spell penetration.
The mastery pages attempt to maximise the damage Yi can do, with the jungle build also featuring the major damage returning and buff duration masteries.
The same idea applies as to the sections before this; get as much AP as possible! In certain instances, Rabadon's Deathcap is a brilliant choice, but I find it is just too much for not a massive damage jump. Hextech Gunblade and Phantom Dancer are there more to increase the effectiveness of his ult. Remeber, though, that late game Yi does not need masssive amounts of AD, so long as you have Wuju Style maxed.
This sequence is used because it just makes the most sense for an AP. The AP components on Meditate and Alpha Strike are considerable, and so the order justifies itself. When jungling, though, max Wuju Style second to assist your minion farm and to also give your damage a consderable boost.
Pretty standard. I can suggest that you may want to switch flash out for ghost if you plan on using your ult as a primary focus.
Once again, I would like to point out that this build is not advised, and I only put it up because it is an incredibly fun build to play. A true 21-gun salute to the destructive power of Master Yi :P.