I think your naming should be fine.because i sometimes use these kind of
naming to populate my list on the server side, I use Struts 2.
I ran into a problem similar to yours recently while doing an Ajax example
for my friend.
What i did was just like seasoup suggested.
you might want to try
$("li:has(:hidden[name^=Theme]).each(function(i){
var subject = $(":hidden[name$=Subject]", this).val();
//...etc for each input
//then reorganize your index in the name of the fields
// maybe create a new html then insert back into the li
})
my selector may not be the best, just so that hopefully you get get concept
