Some stuff was added. See for example: NDK3.9.lha/NDK_3.9/Documentation/Releasenotes/Installer_relnotes
I don`t know of any backwards incompatibility. Maybe others? If you want to be safe then hold both versions for the case the newest version fails for some reason.
About your 40GB drive. You need a proper scsi.device and filesystem to handle large drives. SFS or PFS3 are ok (for details check out the maunals). Thomas has a chart on his site about the limits. It is worth a look. IDEFix patches the scsi.device and it should support also large dirves but I`m not sure. You can use Thomas Check4GB tool to check if your HD setup is 4GB-ready.