I had the same issues trying to view LTV in Romraider from my 3.0r. Just keep using btssm like you've done in the past or use this utility.
The ECU is constantly learning, but can only learn a/f trim and knock control values for a load/rpm cell when it's driven there and when certain conditions are met to put the car into learning mode - i.e. I guess you could say the ECU has "fully learned" once it's been driven through all RPM and load points. Really good info on knock control here.
If you've driven through the rev range and your IAM is at .500 - welcome to 3.0r ownership. They knock on anything that isn't Japanese 100ron that they were built for and even then, looking at their ignition tables, I reckon they'd still ping and lower the IAM.
It's good you diagnosed a faulty part and replaced it, but, you could have the world's best serviced and maintained ez30 and it would still knock on 98ron and end up with a low IAM. The only way to fix this is to tune the ignition and fueling, or, ignore it.
Low IAM won't hurt the engine, it's there to protect it. It will hurt performance and fuel economy though, as you've experienced.