1999 Honda Accord Oil in Radiator Fluid

I purchased this car back in August, it has run like a champ until the heater hose blew. I replaced the heater hose and the thermostat, but noticed that there was what appeared to be oil in the radiator.
The car runs fine at RPM's over 1000. There is no evidence of smoke being vented out of the tailpipe. Since I replaced the thermostat it now idles choppy and will stall, but once the car runs for 5-10 minutes it will still idle choppy, but will not stall. What are the causes of oil in the radiator? I am going to drain the entire system, flush it, and refill with new antifreeze. Is there something else I should look for? The car does leak oil. But the oil it leaks is clean, any other suggestions on how to repair this problem?