Ok, I did regret not getting the tire there.. the other place lied about having the tire.. (when will I learn?)
However, one way or another, I ended up getting tires and parts in Merida at a place called Bicimotos, on the intersection of Calle 59 and Calle 74. Mario owns the place, and speaks excelent English. I was told about him by the Kawasaki dealer in Oaxaca.. who has no KLR parts.
Anyway, tires take 2-4 days depending if you get Dunlop, Pirelli or Avon. Prices are not over inflated (I paid 880 pesos for a MT60 rear, got it in 2 days). Kawasaki parts take 5-7 days although he has some in stock and some non oem parts too, which are a LOT cheaper.
Also worth noting is the fact that they have good mechanics at this place, with the mechanics department being run more like a Euro/American operation than a mexican one, except for the number of disassembled bikes. Hourly rates reflect this, but are still very reasonable. (500 pesos for two guys, one for 3+ hours, the other changing the tire)