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, 4.10's, ARB Bull Bar, Smittybilt XRC 9500lb Winch, 4X Guard Trans skid, Skid Row Engine skid, Factory T-case & Tank skids, Custom BoulderBars, JBA Front Coilovers, OME 948 rear springs, Bilstein rear shocks, JBA A-Arms, Moabs with Goodyear Duratracs 265/70-16