This is getting to be quite the interesting story. I wonder who the Moody that killed Neville really is? Good thing Hermione saved the body. A few thoughts:
1 - Have Peter & Trelaney meet at Hogwarts while both are in animagus form; Peter sounds like he might be looking for a way out of Moldieshort's service and he could provide some important info; though with Harry and 2 other Marauders around, he'd definitely be paying for his survival.
2 - I wonder if Tom saved any blood or tissue samples from his original body? It'd be interesting if Harry contacted him for a truce and asked for such to use with a sample of Dumbeldore's blood for a muggle-done DNA comparison to verify what his grandfather found. Imagine the reaction of Voldy to that.
3 - You have to wonder how long before the Weaseley's wake up and realize just how they've been used. Heh, can you imagine their reaction to getting a letter from Perce and Ron?
Keep up the good work!