The best way to reach The Pit is to take the Outer Cloister waypoint and head back out the Monastery Gate to the Tamoe Highlands. The path leading away from the gate will lead you to it, although you may have to try a couple of different forks until you reach your destination.
The Pit is Area level 85 in Hell difficulty and most of the good stuff in the game can drop there. The Mausoleum in Hell Act 1 is also Area level 85 as are the Ancient Tunnels and the bottom level of the Maggot Lair in Hell Act 2. However not every item in the game drops in these areas. If you want a shot at every item in the game you need to run Hell Baal. Nevertheless The Pit is generally considered the best location for magic finding when you consider difficulty and time spent vs. potential rewards, although a few builds do better in the Ancient Tunnels or Mausoleum (I had a sorceress last ladder season who pretty much lived there). Almost no one MFs in the Maggot Lair level 3 since you have to go through two other dungeon levels to get there.
Check out this guide for exhaustive details on the MFing in the level 85 areas:
http://strategy.diabloii.net/news.php?id=532
As for runes it all depends on what you are looking for. If you want lots of crafting runes and the occasional mid-level rune you want to kill the Countess in the Forgotten Tower in Hell difficulty (Act 1). For consistent mid and high(ish) runes you have to do the Hellforge quest in Act 4, Hell difficulty. Since you can only do this once per character your best bet is to rush people in return for their forge drops. For the highest runes in the game you have to kill Diablo or Baal over and over in Hell difficulty, but the odds of ever actually seeing a high rune drop are still very small. Think of it in terms of winning the lottery.
Evrae gave you a good overview of MF items. To read up on every item in the game and decide for yourself what is best for your build check out this site:
http://www.battle.net/diablo2exp/
Good luck!
