I want to have a set of TrickFlows milled from 64cc down to 58cc (to obtain 10:1) compression on the ZZ4 shortblock). Should i have them angle milled or flat milled? I need to loose 6cc's. The head specs are .008 inches per cc angle milled and .006 inches per cc flat milled. So thats .048 inches angle milled or .036 inches flat milled.

Also what about the intake? Angle milling would change the intake angle of the head. Flat milling i would just need to mill the ends of the intake right?

Flat mill them... A lot easier.

No head bolt hole enlarging.
No reagligning the intake manifold face.

If you only flat mill .036" off the heads you probabily won't need to machine the intake face either.

How much should I mill the bottom of the front and the rear of the intake so that it sits lower. So that it has the same position on the head as if the heads were not milled. If the heads are flat milled .036 inches? Is there a chart that gives values to match the intake milling to head milling?

I had a block that was decked .040" and I ended up using some .015" offset head alignment dowells rather than milling the intake.
About $9 from competition products.

Angle milling would be the wiser of the two as it does take away less material from the quench area and more chamber volume overall as you already know. As F-Bird'88 has said this will cause a bolt hole alignment error of about 0.025" on the long bolts(less on the short bolts). This may or may not use up all the head bolt side clearance. Would also be a good idea to reface the bolt head platforms as they will no longer be square to the block either. They'll only be off about 0.003" which can be tolerated but to be 100% safe it's best to have it done.

Less other problems if you flat mill like was said above. I would call Trick Flow and ask them. I'm sure they have answered that question many times as it is quite common. You might be able to use a thinner head gasket to make up some of the differance. I would not be to concerned if you wind up with 9.8:1 or 9.9:1 compression. Allen