[lots of words]
Option (1): Rebuilding on the Redundant Drive
[still more words]
I think that pretty much sums up my view. If you have an application that is difficult to install, you could build out a new gentoo server somewhere (locally, on amazon, etc) and get it working there. Then take that configuration (you could even just rsync+ssh the whole os over....) to that other drive in your server and reboot.
.r'