Here is the background: I had my car tuned 2 years ago and I've been getting an increasing problem with counts of knock. I started a new job about 2 years ago and my evo hasn't been driven very much. In fact I've probably put less than 10k miles on it since the tune. The knock has been getting consistently worst over time. The car didn't pull like it used too and felt very flat and at partial throttle it felt like it was brake boosting (turbo spooling up but not accelerating). During my investigation I found the exhaust gasket between the manifold and turbo was leaking. I replaced the gasket and the car drives a whole lot better and the knock seemed to go away but as I continued to drive the car around the partial and WOT knock came back. It doesn't happen every time, sometimes the CEL will flash(CEL on knock > 5 via Tehpra Mod V7) at partial throttle between 2500-4000 RPMs and same with WOT, sometimes it will knock, sometimes it wont. The car doesn't show any hesitation and pulls strong again after the gasket replacement but knock persists although a lot less than before. I've boost leaked tested the car and replace the spark plugs. Before I replaced the gasket the AFR would run super rich 10.0 after the gasket replacement the AFR is holding steady around 11.1-11.3.
Car: 03 Evo 8
Mods:
HKS280 cams
Stock turbo
Stock block
Stock head
Intake/exhaust
ETS Intercooler
Turboxs piping
Greddy RS BOV recirculated
FIC 950cc
Walbro 255lph

I've included a log I took while cruising around and a 3rd gear WOT pull. Any thoughts would be great!

 

Can you try taking out some timing in the problem areas to see if that mitigates the knock? Have you tried contacting the tuner that tuned your car perhaps they can decipher if its real knock or false knock you are experiencing.