If the timing marks line up it could be either the cam or crank sensor is bad. Both are on the right side of the engine; the cam sensor is easier to get to.
Start there first - my other ideas would require some disassembly :-(
P.S. What year engine are you working on?
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2003 Renegade, Black
- 3.7L, 42RLE, 4X Guard Trans skid, Factory Engine, T-case, Tank skids, Modded BoulderBars sliders, OME 927/948, Bilsteins, JBA A-Arms & 1/4" top plate, 2-ring clevis, 1 extra rear iso/side, Moabs with Firestone Destination AT's 255/70-16. Future: 4.10's