Go ahead and install/enjoy the Flashpaq tune now.
When you install the exhaust later, just follow this procedure to force the computer into "quick learn" mode. It will basically clear out long-term fuel trim memory and re-build the fuel trim memory more aggressively than normal (probably other things I don't know about as well)l:
http://www.quadratec.com/jeep_knowle...article-89.htm
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