mine started doing the same type of thing, but early on when it was running pretty well it had a high idle (3000ish rpm) then started bogging, I would make a run at a hill no problem come back down at idle then it would barely idle, touch the throttle and die, then I figured out if I just mashed the throttle it would bog for a seconded then take off, like it was trying to flood the motor but it took off not like it was trying to clear out. I have a 09 m1000 with slp pipe, bdx intake, bdx oil delete, BD box, PCIII, and all slp clutching. I tryed adding fuel with the bd box but either direction and it seemed worse. finally got pi$$ed and crank my Fuel Pressure up 3 lbs then added the full 10% at low range on the PCIII (all you can without a lap top on the PCIII) then added 5 at L 3000 on the bd box and 3 at mid 3000. after that the bog was hardly there and it worked good ( slight hesitation but not real noticeable). I will have to see what happens next time. probably wont even start now.???? I just got the PCIII so I am planning on putting the stock intake back on and run it to slp recommendations to see what happens and if there is more or less power, and work from there. But the PCIII is preprogrammed by slp for there setup and having to add more fuel on the bottom and top makes me think its getting more air with the bdx intake which should mean more power but will take some tunning.
I think with as much of a change as I had to make something is up, may be the stock pipe sensor is going out.