It shouldn't have any effect on the ignition timing directly, but it could affect the idle speed because of other factors influenced by the exhaust and thus indirectly affect the timing due to those such as a change in backpressure and mixture readings by the O2 sensor. It wouldn't hurt to check the timing though. It should be set at 5 btdc with the engine diagnostic t1 and e1 terminals jumpered together. Also, the idle speed needs to be adjusted to where it's supposed to be, 750 with a stick, before you can get the timing set accurately. If getting the idle and timing dialed in don't change the idle quality, the egr valve could be suspect or as mentioned the cat could be plugged.
*edit- when you jumper the test connector, the engine speed should noticebly drop. if it doesn't the throttle position sensor may need adjusted as well:
http://4crawler.com/4x4/CheapTricks/TPS/index.shtml