I'm pretty sure the old ke10 gearboxes had a smaller spline clutch kit. No biggy though, just put the original 3k flywheel and clutch kit onto the back of the 4k.
Apart from that everything should be fine. You might however just want to swap some of the 3k ancilaries (water pump, thermo housing, alternator etc) to make you're life super easy and they do change slightly.