Updating firmware...FOREVER

I did not unzip the file before I tried to upload it. Since it didn't take it, I followed up with just letting it do it remotely (first time for doing it that way). I figured the remote method would be somewhat automatic but it hasn't worked out that way.

This morning I unplugged it and powered it back up. It has been about 20-25 minutes and it is still booting up (still says 'booting') via Raidar too. The blue light is still blinking once a second but the two drive lights are solid and the green ACT/DCT (or whatever that light is) isn't on at all. The drives are grinding away which wasn't happening last night. I'm hoping that this is a good sign and I have not bricked this thing.

I am wondering if the growing number of sector errors on one of the drives may have a hand in this (?). Any ideas of how long I should wait or what I should do next? Would it help if I removed the drives and tried to boot?