Right my friend uses Rohan, and has gone for a complete 400 points calvary army all with throwing Weapons w/ Theoden.

Im using my 400 points elves:
Arwen W/elven Cloak
11 warriors w/HA
11 spearmen w/HA and Spear
11 Archers w/HA and Bow

I know that if i can get arwen to use Natures Wrath, ive almost got the game, but my question is:

How do i protect Arwen from the throwing weapons when he charges with the Calvary?
(obv she still be at the back of the force which will make an in the way test)

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Hey, how you doin (:

If he's close enough to throw at Arwen behind a shield wall, he's close enough to be charged. If you're infantry and you can charge cavalry, you should almost always do it.
If he's charging and throwing, I believe he can only throw at the model he's charging, so there are no in-the-way rolls.
Other than that, elf cloak and in-the-way is about all you can do.

BTW, you can take the sting out of the charge by shielding with those who do not have spear support. With elves, odds are with you if you can match dice.

Also, since elves are such amazing archers, I'd recommend using them to eliminate the horses. That way you have to worry about them causing so much damage to your battle line.

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Mordor summons them. Vengance drives them. Hatred lends them strength. Gondor will burn.