Det 1

I may have found the problem (fingers crossed). At the suggestion of AirGabber and browndg, I cut the tach wire on the remote start. We drove nearly 400 miles yesterday and today without a hitch. The truck seem to run smoother and shift better. It's difficult to know if the program put in by Smarty Jr. or the lack of the tach wire connection is the cause for improvement. I have about three options on attacking the tach wire issue. I'll continue to post until I'm sure it's fixed.

AirGrabber

Well thats good news! And it sounds like your gonna buy a smarty too.....
To basically answer your initial question, the crank and cam sensor work together at start up, ecm uses crank signal and cam sensor is more or less a back up after that unless initial reading from both are out of tolerance, which is why the truck will still run ( most of the time and may miss) when one is bad, or unplugged, but will illuminate the problem light on your dash. The tone ring mod, although effective, will make the ecm use both sensors as it senses the timing is out of tolerance and corrects the difference between the two.

Det 1

Yeah, I'm pretty sure I'm going to buy the Smarty Jr. I don't trust the stock lift pump so I'm going to back it up with an Airdog Raptor 100. I'm still not sure why the tach wire on the remote start would cause the problem since it only senses a signal. I presume it's spliced into one of the sensors. In any event, my options regarding the remote start are to change the connection to the other sensor, check to see if a "virtual" tach sensor will work, or to interrupt the tach wire with a switch that could be turned on to allow remote starting of the truck and turned off so the truck will run properly. I should know within a couple of days.