I physically installed a second hard drive in my MKII empeg but I don't have the ability to make a serial connection to the port to get shell. I have ethernet connectivity only.

Is there a way to make the unit recognize the second drive without shell? If not, is there a way to get shell on the player without serial?

It currently has the latest hijack kernel.

Uh, tricky. You either need a serial connection (console) or you need to load a telnet daemon or rsh or some other communication package that is not there by default. I strongly recommend trying for serial console - knowing that it sounds like you do not have the ability to do so at the moment.

You might be able to use ftp's exec commands, but I am not sure if it will give you enough flexibility to build a secondary hard drive. Basically, you would have to do this and then this to partition and build the secondary drive.

You might also be able to create a script with the proper commands, send them to the player and execute them with the ftp daemon. See this thread for a description of doing this with a slightly less complicated case.