Hi Tony, congrats on the new acoustic! Acoustics are great and yes, sometimes, usually, a bit harder to play because of the heavier strings. In answer to your questions:

1) For muting, I am primarily using my right hand to "slap or pat" the strings on the second upstroke. The left hand can relax a bit on this beat, but it's not necessary.

2) Practice the intro as slow as you need to to get it clean, then gradually speed it up while maintaining the clarity! Also, make sure that you are using alternate picking.

3) Yeah, they don't call it the "F" chord for nothing ;) You can try turning your left index finger a little bit so that you are using more of the boney part. You can also try moving you left index finger a bit higher or lower on the neck to see if that helps. Sometimes the string falls into the joint and gets muted.

Good luck, I hope this helps! :)

Cheers, Tom