You dont really need to refresh the kext cache when you exchange a piece of hardware, if you have a valid kext installed it will be loaded as soon as you plug in the new hardware.
Your post is very confusing on the details (did you switch from IDE DVD to SATA or you use the same IDE DVD in a new controller?) but you should find out which kext you are using for the IDE & SATA and try to find an alternative one.
If your SATA drives are being detected as ATA you are probably using AppleVIAATA or similar catch-it-all kext which might have troubles with SB700 (less speed and no NCQ of course). Try switching to AHCI and it should improve a lot. As for the IDE I dont know which kext supports SB700 IDE ports, there was some AppleATIATA port but I'm not sure if the IDE controller in SB700 is supported.