I have no idea how the HKS Ignition System works but spark is directly related to this issue. Does it have full voltage to it?
Try splitfires and standard ignitor etc. Back to basics. Its a longshot, but possibly the IGN system is faulty and not burning all the fuel that is going in, but burning just enough to make the power, and blowing the unburnt fuel out the back.
The AFR meter will only read burnt fuel.
I cbf reading above but how is INJ duty compared to the last tune exactly?
If higher than last time more fuel is going in, but if its making the same power and running the same AFR as last time, somethings up.