Update to the issue I posted above. Don't depend on toyota to fix it and the dealer folks are almost clueless because they have not come across this issue before. Spent one full day at the dealer yesterday.
Solution is simple. Do the pilot injection quantity learning (this is what I did and not learning detail) and it fixed itself. Now there is no rattle sounds like new and the throttle response is also good. I did this with techstream and I believe the same can be done by scan tools like Gscan and launch.
Took the vehicle to the Toyota this morning and showed it to them
Also note that if the injector/ecm/engine is replaced it is not enough that the compensation codes are entered. Pilot quantity learning has to be done, this is as per workshop manual.