It runs smoothly idles great until I turn on the heat or ac then it bounces like it was cammed every now and then kind of hiccups at highway speedsWhat brand CPS? TJs can be picky about that and Mopar is generally the recommended brand. Make certain that the sensor's wiring is intact and well grounded.
Can you describe how it runs? Any driveability complaints? Has it thrown codes since the engine was installed?
Since it's a new engine, it's not likely that the chain is bad, but you could ask the engine rebuilder about it to make sure. The FSM has a procedure to check for stretch.