So after pulling the sc and water pump today I reconnected the battery to put the windows up and it was good for like 10 seconds and then lost all power to everything ....i think something may have shorted out ? Any ideas on what it could be and where to look.... I'm thinking the alternator wire may have grounded off on the block as it was off and hanging :/

 

Try making sure you have good connection on your battery. Test battery for 12+ volts,
There is a large fuse with the battery. If water got into the battery box, this fuse can get weak and fail. Also make sure all the positive wires near the battery are clean and tight.

 

Check the ground in the engine compartment.

 

That is the big bare one on the passenger side next to the engine mount.