Hayden,

How hot? - I just dissembled the batterry, several connectors were burnt - mind you they look like thin aluminum.

1) I have tripple checked for pos and neg - It looks good to me. I put deans connectors on the batteries, and they were working fine with the titans. I think the UBEC is set up okay too.
2) see above
3) I am unsure what the two mean - the pack was made with three cells in a straight line then a straight line up parallel (I am assuming it's this). Each cell did have small peice of aluminim concecting each other.

The caps are what the ESC came with - I am unsure of their purpose...I am pretty new at this.

Here is a very basic diagram of the set up