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Jolt doesn't stand a chance against Mewtwo. Actually, not much stands a chance against Amnesia-Mewtwo; Parasect can hold its own, IIRC, and GBL has had a Beedrill get lucky (don't count on it, though), but otherwise... The best you could do is get it to sleep, but Sleep-moves are generally luck-based.
I don't think there's a reliable counter, but the only ones not mentioned that might work is Tobybro ... or another Mewtwo. Smogon has a little blurb about "counters" for it: http://www.smogon.com/rb/pokemon/mewtwo
Seriously though, Mewtwo is so overpowered in RBY, shouldn't this tourney have banned it?