I'm really not up on LiPo, but then nor is Boeing 
I understand that individual cells within a pack need to be charged individually, and that one should not charge cells that have dropped below a certain voltage, nor mix cells of differing voltages. But I read that a long time ago and it may not apply to current cells. (something else to do!)
Edit
This looks readable Complete Guide to Lithium Polymer Batteries and LiPo Failure Reports - RC Groups
Edit, Edit
Mmmmm, quite old "Winter 2005" But worth a read, Check out the lower end of the post if you want to be put off.
I've had a look around for home-brew chargers, but not found any I'd recommend, but there are many low price units out there (if you have a multi pack, get a balance charger). As with NiCd's it's the RC peeps who are pushing with LiPo so go read their forums.
Many years ago I used to make fast NiCd chargers for RC clubs, I always supplied them with metal charging cages due to the possibilities of explosion & fire!
It looks like the first part of your project will be a battery management system... Something for your Masters degree 
Then you can get a job with Boeing - even the big boys get it wrong.