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Does it matter if it's been sitting for an extended period of time or not?
What color is the smoke?
Blue smoke does indicate an oil issue. This could be the oil rings or the valve stem seals. On rare occasions I have seen the actual valve get a hole in it and cause some pretty massive blue smoke.
I think what I would do here is a compression test, followed by a leak down test. The compression test will tell you if there is anything MAJOR going on with the cylinders. The leak down test will check for smaller issues like a problem with the oil rings. If it's been sitting a while, the oil rings could be locked up on the pistons and not scraping the cylinders, this would allow the oil to go past the rings, burning it and fowling the plugs causing the rough running.
I would do these tests to try and make sure the inside of the engine is in good working order.
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This type of issue seems more like it would be a distributor or ignition coil issue then some type of ring issue. I have seen the coils get hot and stop generating spark. Then after it cools off the wiring in the coil sort of re connects and it will work again.
Is the question about smoking and a rough idle or about the jeep not starting after short trips?