External hard drive doesn't wake up fast enough for Time Machine

I am having trouble with using SuperDuper and Time Machine doing their jobs with my external firewire drives.
Config: One 750GB drive (one partition called DataDisk) and one 1TB drive (with two partitiions - Clone and TMDisk) connected thru daisychained firewire to the mac mini.
*Backup Strategy*: SuperDuper clones the internal hard drive to the Clone partition once a week. The Time Machine is setup to backup the DataDisk to the TMDisk.
Usage: My Mac mini is essentially a media server with iTunes always running. Per advice on another thread, I have the mini's power saving setup to let the hard drives go to sleep when possible.
Problem: Once the external drives have gone to sleep, and the SuperDuper tries to do the cloning, it fails. Similarly, the TM fails to find the backup drive. However, if I keep the drive active at the time of these backups, both SD and TM work fine.
Is there a way for me to wake up the drives before SD starts its cloning? Note: I am not letting the mini go to sleep as I use Apple TV to play its contents remotely.
Also, is there a way to wake up the drive before TM starts its operation every hour?
Appreciate any help.
Message was edited by: new2appletv

Hi Andy,
Thank you very much for your suggestions.
I will try to test with USB connection. I will try with the 1TB drive first as the 750GB drive needs work. The 750GB drive needs the firewire interface card to be replaced by the USB card whereas the 1TB has both available together.
I am not terribly in favour of keeping everything ON for the following reasons:
1. The mini or the drives make a whirring noise all the time that they are ON. One of the reasons, I retired my windows PC is that it is inside a computer armoire in my bedroom and even then the noise from the SMPS and CPU fans drive me crazy.
2. The TM starts a backup cycle every hour even when there is nothing to backup and this causes clicking noise from the drives. If I could configure TM to run only once a day so that I can get the rollback uption (which SD can't) when I accidentally delete some data file. But, I am told that TM can't be configured thus.
3. Power consumption: I have a power meter that plugs into the AC outlet into which I can connect the devices under measurement. I will find out how much power it really consumes. I had purchased this device to measure the power consumption of the pump/filter in my Koi pond as that runs 24/7 and I don't like drawing too much of electricity as it is a scarce resource today (the electricity cost is also very high in Northern California).
I am just wondering if I should buy one of those RF remotes that you connect to USB port which can operate from upto a distance of 60ft. I could keep this next to my Apple TV remote and use it to wake up the mac mini before using my Apple TV. I only hope that the mac mini wakes up on this type of remote as well.

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