The IDE delay is built in, so there's not much you can do with it. If you don't have anything on the IDE channel, then the timeout will be much longer. You can build an adapter that tricks the interface into thinking there is a device on it if needed. Otherwise, the drive spin up delay isn't a big deal. I don't even notice it.
BlizKick from Aminet can apply all the 3.5/3.9 system patches, as well as move the ROM to fast RAM, with one reboot. Check it out on Aminet.