If the bike has older (VERY lean) maps in it, of course the aftermarket exhaust will cause it to be even leaner...!
Yes, this could cause your failing to run.
Also, the warm-up maps could be off.
Take it to your nearest Harley/Buell dealer and have the latest maps installed (flashed !) and see if that does the trick.
In any case, even with the latest maps from Buell, with the different exhaust, it should run...but it wont run like it should.
One thing to think about, call Erik Buell Racing and see about getting their ECM. Tell them "everything" about your bike when you talk to them.
Should make a big difference.
Mike