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I don't think so. According to the rules, you can use a magic ki focus to add its enhancement bonus, critical hit effect and magical properties to a weapon attack. Nothing more, nothing less. The extra reach from a Transcendent Ki Focus isn't a magical property, so you wouldn't add it to the weapon attack. 

By that line of reasoning, you wouldn't gain any benefits of any superior ki foci when making weapon attacks...

I believe it is added.

A superior implement is not the same thing as a magic implement, so different rules needs must apply.

For example, take the feat and buy a non magical transcendent ki focus. You now have no magical properties whatsoever, and you are not wielding a magical ki focus.

[edit]
Let's look at the actual and full rules text from which you're getting that from;

  Ki Focuses and Weapon Attacks: If you use a magic ki focus, you can add its enhancement bonus to the attack rolls and the damage rolls of weapon attacks you make using a weapon with which you have proficiency. If you have both a magic ki focus and a magic weapon, you choose before you use an attack power whether to draw on the magic of the ki focus or that of the weapon. Your choice determines which enhancement bonus, critical hit effects, and magic item properties and powers you can apply to that power. You can’t, for example, use the enhancement bonus of your ki focus and the critical hit effect of your magic weapon on the same attack.

Note that is only diferentiating between which of the two you get when using a magic ki focus and a magic weapon. It in no way has anything to do with superior implements.

I do believe that the OP would indeed get reach 3 with a transcendent ki focus and a kusari gama.

Well, I think I do get the point of Hephalumph, though.
The rule only applies to magical properties, but not the weapon characteristics itself.
The reach 2 of the Kusari Gama is not a magical property, but a general.
The Transcendent Ki Focus applies a +1 to the weapon reach, so theoretically it could also apply this to any other
reach 2 weapon, as long as you use your Ki Focus, since general properties seem not to be deactivated by that rule.

Also there are magical superior implements like a "Transcendent Manual of Ninjutsu +2" for example.
However that additional +1 reach is is superior, not magical. So is the reach 2 of the Kusari Gama.

That was my original thought at least.
Thanks for your contributions so far.

Feb 1, 2012 -- 2:34AM, thespaceinvader wrote:

Superior Implement bonuses NEVER apply to weapon attacks.  This is specified in a sidebar in the book that released them.  So no, the +reach from transcendent will not ever stack with the reach from KusariGama.

So you can use that +1 reach only when fighting with a Ki focus and bare hands (unarmed). Like some monks may do.

Feb 1, 2012 -- 2:41AM, thespaceinvader wrote:

Unless the attack has the Implement keyword, the Superior properties do nothing.

ALmost all monk attacks are Implement attacks.  The Superior properties apply.

And what about powers, which include both, the weapon and the implement keyword?