Brother it has something to do with air intake and exhaust of the car maybe the car is not creating enough Vaccum.
Check the airbox / air intake and silencer very closely for any air leak.
Also check the brake booster.
The silence guy must have removed the CAT converter.
Have u connect the ECU to the OBD-II scanner for nay fault codes?
Have u changed the engine mounts or gearbox mounts ?
There was no need to change the iridium plugs they last for 50000 km easily.
First determine whether the vibration is from engine or from gearbox I do not think that its something with the eingine because 1KR FE is one of the best engines in the world.