Hi Salman
I'm a long way from being an expert, but I do want to express a big caution ... ...
1. A little googling suggests your batteries might be Lithium, which I think requires a particular charging system to be safe
2. The spec of your Transformer would suggest the output is AC not DC which your batteries require and this might explain why the diodes are getting over hot.
I may be completely wrong , often am, but until someone who knows better jumps in and gives some good advice, please be careful because I think what your doing at best, will damage your batteries; at worst, will cause an explosion !
S