xj problems

well, First my water pump died and fried the head gasket Installed a new water pump and head gasket, I put everything back together, when I was doing that I noticed my fuel injectors had a ton of blackish crud on them I cleaned them with injector cleaned, I used the sea foam stuff, and soaked them in it, I then sprayed some WD-40 on and into them like the jeep dealer told me, reinstalled them, now my check engine light is on. I pulled the codes and I get:

1 - Battery is disconnected (I have no idea how this is possible)
2 - Injector Control Circuit
3 - Radiator Fan Relay
4 - Improper Charge Temperature Sensor Voltage
5 - MAP Signal Fault

I have no idea where to start...

Thanks in advance guys...
- Matthew