The server is working now! I called Apple Support, but the technicians no longer have documentation for this server. I tried taking out the hard drive board and power board and put them back in and made sure connections were tight. That worked.
One time when it booted up, it booted up fine with Red-Green-Green-Red on, but those went off when the cover was put back on.
As for Hard Drive Bay 3: there was one time a couple weeks ago when the empty tray in Bay 3 did not light up. Now any empty tray I put in Bay 3 will have a solid yellow light for a minute or two, then stay solid red after that. I won't be using that bay so that's not a problem (if the whole hard drive card doesn't fail).