the Dhak sound is there, It's because the car is raised beyond design specification, however, it should not be bumpy, even on stock tyres, please check your tyre inflation, some pumps have Chinese digital gauges that over inflates the tyres and that's what make the car bumpy.
As for the Dhank sound, it eventually reduces as you adapt to it, you will soon find the parity when you start crossing potholes at a speed where it does not sound that way!
Changing the tyres and moving to 195/65/15 was really helpful in my case, Advan DB V552 are good soft tyres, I have them on my Aspire, but on Yaris I am using Dunlop Touring R2, I would say that for Yaris, consider Continental, as it already has quite soft suspension, Yoko's would be an over-do,
