It could be that the BIOS is examining and scanning the external hard drive so it would be wise to try to boot up with the external hard drive disconnected and see if your boot time is significantly reduced.
In fact with your USB external drives powered-on, open the BIOS and look under Boot order. If any USB device is listed, disable it. If you ever need to boot from a USB device you can always change it back.
I checked BIOS and there is no USB listed in the boot up list.
Also I went to disconnect my external hard drive only to find that my son had already done so at some time *(I've not been backing up for a while!), so there has been no interference from this.
Now the computer no longer seems to boot automatically even after waiting. I turn it on - nothing happens - I leave it for 15 minutes - nothing - press 'on' again and it kicks in like you would have expected with the first push of the 'On' button.
If you're happy working inside 'the box', I'd pull out the main 20/24 pin mobo connector and then use a bent paper clip to short pin 14 to 15 (that's green to black - any black will do). The fans should spin straight away (you're just replicating the front switch). If there is no immediate response, then I'd suspect the PSU. If there is, then the front switch or the wiring could be at fault.