i have a 97 contour zetec engine. i milled the head

not long ago because it got warped. runs great when the engine is warm or its warm outside but when its a cold engine and cold outside it runs like crap. it will make a knocking sound until it warms up...the colder it is outside the louder the sound. also the lower the octane gas i use the louder the sound. i know milling the head causes the compression ratio to go up...is there a mod to do to compensate for this?
does it sound like i need to retard or advance the timing?
is there a way to fool the engine into thinking the air temperture is different from what it really is?
any suggestions
Thanks