think that your timing belt tensioner may have run out of tension and allowed a tooth to go by...notice how the kit has a tensioner...this is just a guess,...but the only other guess would be a fuel pressure regulator~
It being a '97 with who-knows how many miles, it could also be a clogged catalytic converter. Protege's also have a known issue with the intake hose developing splits too. You'd need to take it off completely and do a full inspection.
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