Try re-entering ALL the parameters.
Low/dead batteries could have "hurt" the RAM which are keep alive in power down mode. The TTL memory runs on 5 volts but the batteries only supply 4.5 at best, 3 or less when low/dead. This is at or below the low limit threshold of whats needed to keep TTL memories alive.
You might also want to clean and reseat ALL the connectors to the various panels and mother boards. These get loose and can cause some real nightmares.
Check for blown fuses - especially in the drives. Phase errors will blow them as soon as you power up and blown fuses, especially the ones with tell-tales will preent READY from happening. If you do blow fuses at power up, switch any 2 phase leads - this usually fixes that problem.