ToT trash will only give rep to 2999/3000 Neutral. If you get the quest for the 3 ritual stones from Taran Zhu or pick up a Key to the Palace of Lei Shen, don't turn them in until you're to 2999/3000. Turning one in will then bounce you to friendly to buy the Friendly rep items.
So far there seem to be 4 quests for Shado-Pan:
Treasures of the Thunder King - 500 rep (completed after your first "treasure room" run)
Secrets in the Isle of Thunder - 200 rep
Setting the Trap - 300 rep
Champions of the Thunder King - 300 rep.
The last one supposedly is repeatable once a week so even someone who doesn't raid at all could get to exalted with Shado-Pan Assault eventually - if you have 130+ weeks to spare.