Picked up an 07 superglide the other day, 2 into 1 big radius, pops like shit on decel, but ill look into that. anyhow i looked at the standard pipes that came with it, wtf is that spring loaded butterfly  thingy on the rear pipe and also some black box. it was in the box of goodies that came with it.  stuffed if i know

That is the active exhaust valve, or "flapper" as it has become known.
The black box is(assumably) the control unit, or "actuator".
There is most likely a short cable there as well?........... that connects the 2 together when fitted, for normal operation.

I imagine that either you have some kind of tuner device that allows you to "turn off" the active exhaust feature in the ecm, or there is a "tricker" installed(a small device that is plugged into the wiring harness that was originally connected to the "actuator" that you should be able to see, behind the rear pipe above the starter area) that makes the bike think that the unit is still connected and working. Without either of these methods methods employed, the engine check light would glow, to indicate something
is (in this case) not working correctly.