Go to your SH4 \ Data \ CFG \ Commands.cfg file.
There is a long list of commands, so use the Find option, under edit, or I think it CTRL+C on the keyboard.
Look for the "Y" with quotes. The one you want will say Cycle Aft Tubes.
At the front of the line, it is commented out with ";". Remove the ";" from the front of the line, and you will have the Y key back for cycling the tubes.
You can do the same with the letter "E", for a key command to blow ballast.
That should get'cha back in business.