Your car started overheating after you did all that work because the Ka is a pain to bleed all the air out of the system. When you fill your car back up with coolant, air gets trapped in the system. So many guys have problems with it, and it can be a bear if you dont know the tricks.
You did bleed the coolant through the bleeder bolt when you filled it up right?
You need to jack the front of the car up, and run the engine for 5-10 min with the radiator cap off. Make sure you have a bucket or something underneath it to catch the coolant that drops. This will normally get all the air out, if not, the next time you drive it it should be fine.
Your heatercore having brown coolant in it is another issue. Thing is, your car didnt overheat before you did the work, so logically what you did is the cause of the problem. Try turning your heater on full blast and running radiator flush through your system. Follow the directions on the bottle when you do.
Also, the brown stuff is rust. If your coolant system has rust in it, that means that your coolant isnt mixed right, it has to much glycol in it. Or it means you have waited wayyy to long to change your coolant.
EDIT -
shredmaster47 wrote:my 95' 240 sx se is overheating after i replaced it with a new radiator, and new thermostat.
Ohh you mean your car was overheating, then you replaced your radiator and thermo and it still does it.. Yea, then you have a clogged heater core. Still, try to flush it out before you do anything drastic, changing the heatercore is a PITA.