Kaen is just as powerful an opponent in 3.6.0 as he is in previous versions, but scrolls of scare monster now affect him. Therefore the easiest way to deal with him is to drop a scare monster scroll on the upstairs as soon as you arrive on his level. He will wake up and teleport to you, but he will be unable to attack you directly or flee upstairs, and he will not move away or cast spells (except possibly to heal himself). You will then be able to beat him to death in a matter of turns, preferably using F to ensure you stay on your square. Watch out for other monsters zapping wands of fire and possibly burning the scroll from under you.
Because of this new vulnerability, a Monk equipped with one or two scare monster scrolls can probably complete the Quest once it is unlocked, and does not need to wait until after finishing the Castle.
Kaen is incredibly ferocious in a straight-up fight. Fortunately, he has weaknesses, and a wise Monk will exploit them – in the words of Sun Tsu, "You may advance and be absolutely irresistible, if you make for the enemy's weak points." Kaen's weaknesses include his predictable behavior (teleporting to the upstair to heal), and his lack of key resistances (sleep, level drain, and disintegration). The strategies listed below generally strive to play upon these weaknesses.
Even with a good game plan, you may find Kaen a deadly opponent. You will want a very low AC to degrade his attacks (-20 is comfortable; you may get by with less), enough HP to survive multiple rounds of combat against him (200+), and a very high Luck (remember the altar you get on the first Quest level) to ensure that you are able to hit him. All of this – and the strength of the other enemies you face on the Quest – indicates postponing this battle until you have had enough time to prepare for it. Generally, you will be strong enough after you have finished the Castle and retrieved the luckstone from Mine's End.
Paralysis or sleep
Wield or throw a potion of paralysis while wearing a ring of free action or zap him with the sleep spell or wand. Make sure you can use this method multiple times to ensure his immobility – you may miss, or he may wake up before you finish killing him.
Sleep is a keyword to defeat him even at level 14 – it is difficult to overstate the power of this lowly spell against Kaen. After rendering him helpless, be sure to hit him hard. Mjollnir is an excellent choice if you have it, as are the martial arts at Grand Master skill level. But one or two of the stronger attack wands, such as Lightning, Fire or Cold will work nicely as well. About 12 shots total should suffice, again assuming your luck is sufficiently high and you don't have too many misses.
A scroll of earth (preferably blessed) will create a safe barrier around you that Kaen can not cross. You may then use any ranged attacks such as spells, wands or missiles (excluding force bolt/wand of striking, which will destroy the boulders). As Kaen lacks long-range attacks, your only hazards will be the Xorns and Elementals, which can phase through the rocks (though Xorns and Elementals both respect Elbereth), and any attack wands which might be randomly generated and used by a monster. You will have to cope with his ability to port to upstair and heal himself, and escape upstairs to the next level – so building a fort on the upstair yourself is a good approach.
Use the drain life spell until he croaks. It is a good idea to do this on the level above and when he teleports away (to heal the modest HP damage that drain life does on top of the draining effect), go downstairs to heal yourself, preferably on a burned Elbereth. Eidolos uses this method for his instructional ttyrec posted on RGRN. The ttyrec can be found here.
Use fireproof water walking boots while fire resistant or levitate over the lava and use ranged attacks and attack wands. At a distance, Kaen only casts the heal self and create insects spells. Beware of losing your ability to levitate – as from lightning destroying your ring! If you levitate over lava, Master Kaen cannot reach you.
Although Master Kaen gains magic resistance from the quest artifact and is thus immune to wands of death, he is not immune to disintegration. Polymorphing into a black dragon and using #monster can allow you to kill him very quickly and easily, though it's important to note that his exceptionally low AC gives him a decent chance of dodging the breath attack. Because of his AC, it's safest to attack him under the assumption that you will miss the first few shots, and thus have positioned yourself at an appropriate distance from him. If you are reduced to 0 HP in dragon form, you will revert to your original form, and should have a backup plan of escape (or attack) ready. To be extra safe, polymorphing can be combined with the levitation strategy mentioned above because of the dragon form's natural flight, though flying over lava as a dragon can be risky as if the polymorph wears off, you'll lose the dragon's flying ability and die in the lava, unless you have some form of backup levitation/flight that isn't removed by the polymorph. Alternatively, you can combine the polymorph with the boulder fort strategy, which is less risky but requires more preparation.
Fight Kaen mano-a-mano. Not recommended. Master Kaen has a higher base damage than any other monster, resulting in very stable and impressive damage, compounded by the monk's high AC. You are therefore opposing his strengths with your weaknesses. Sufficiently advanced players have managed to do this, however. If you decide to go this route, make sure you have high health, low AC, and if at all possible, half physical damage.
In SLASH'EM, the potion of invulnerability turns Master Kaen from one of the most dangerous enemies into one of the least. Additionally, liberal use of techniques, such as Chi strike plus Elemental fist plus Pummel, has been known to kill Master Kaen in a single round of melee.