What could be causing my manual 97 wrangler to sputter and not accelerate?

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After a few seconds, it's like it engages and will resume but runs rough. This started happening after the throw out bearings were replaced.Vacuum hoses are fine.Replaced o2 sensor, plugs,wires,rotor,dis.cap, map sensor,fuel pump. Check gauges light is on, get codes po108, po171.Check engine light is not on. Cat. converter was replaced about 8 years ago in recall.Please HELP!