Why malphite mid you say? Why build him AP?
Well simply because he scales massively with AP, and it's very uncommon too see malphite mid which makes it harder for your opponent to know what you'll do.

When you choose masteries and runes it's mostly up too you. But if you can get some mana regen and such from both your masteries and runes you should be able to use my build to its full effectiveness without having mana problems. I use runes that gives me 2.8 mana regen and that's enough for me so i dont run out of mana, but the masteries are essential or else you will get mana problems.

Are all your own preference. Most people go for Flash + Ignite, it's effective yes but fun? No.
Flash in my opinion should be removed since it is way too powerful in my opinion though, but take it if you soo please too.

Ghost is very effective as you will be ganked a lot in mid lane (Because you are relatively slow, you really need that extra boost of speed), also very useful if you need to finish that low health champion.

Heal i usually take since it's kind of a weird pick and very unexpected among some players. Also lets you stay on your lane for longer so you can time your minions so that you'r turret doesn't get damaged while you are gone. Or you can choose teleport if you wish.

I start with Dorans Ring so i can harass without thinking about running out too quickly of mana. I then upgrade too Sorcere's shoes and the too Haunting Guise for the magic pen for early and mid game, BUT if you are really fed on minions and/or kills you should rush a Rabbadons Deathcap so you can demolish your enemies with ease.

Then go for a Zhonyas Hourglass, the active effect is extremely usefull as well as it gives you much needed armor and lots of AP.

After that it's pretty much up to you, for late game you can get yourself a Void Staff since your enemies will surely be full of magic resist by now (Or they should at least).
Go for Rylai's for your last item.

If the game goes on or if you get more gold after you've finished your build. Then you can sell Haunting Guise for some more survivability and your Sorcerer's shoes for Mercury's shoes so you can more easily escape CC and so on.

Glad you wanted to take a look at my build. It's my first so i have no idea of how it'll look like or how good it is xD

I hope I've given you a sufficient build which you can have fun with :D I swear, it's really really awesome to just mindblow your opponents with this build!