Good description chicknstripn! I was trying to figure out the best way to explain the issue is 99% probably not the map he is running but some other problem that needs to be addressed. My "for example" was trying to elude to any number of issues with the bike could be causing this and that is just one of many that it possibly could be, yours is another one and it is going to need to be pinpointed to resolve the issue.
Joejo, there are many XB's running around with the D&D/K&N combo with no dead spot, I run both of those on an 07STT and 4K is where the bike lifts the front off the ground for example on the "race" maps. Just take a step back and try to replicate the dead spot over and over looking for a pattern, that is how it sounds chickstripn found it was 3rd gear on his, you may find it only does it when engine is hot or cold or something for us to help you out. Run a data log once you get your replacement, maybe someone can see something from that. If you could capture it on video that may help as well... just throwing out ideas.