How to remove as much rust as possible?

[sauminator]

I went to replace the coolant in my 93 gsx, and when looking in the thermostat housing, it was full of rust inside. As well as the thermostat itself. I replaced both and also put on new gaskets. When I initially drained the radiator....nothing but clear water, no discoloring. I decided to run some prestone superflush, following the instructions on the bottle. I refilled the system with prestone and have had no overheating issues whatsoever.
I just want peace of mind though, and would like to rid my system of as much rust as possible. Any suggestions? Or will my car be fine?

 

[92AWDHX40]

It should be fine as long as nothing is bad internally.

 

[sauminator]

Im assuming the rust and corrosion was from the previous owner using regular tap water?