I have removed the heater system and want to know if it's best to run a hose from the coolant pipe above the exhaust manifold to the conection point on the intake manifold or block of the output on the water pump and cap the intake manifold?

It seems that coolant flowing through the intake manifold can, if nothing else, aide in heat transfer on the intake.

Capping both ends reduces the chance of line breakage and water loss.

Any sugestions?

I still have a functional heater in my car and am thinking through the process of removing it as well.

you can make a plate to block off the head and use the stock gasket- i suggest either taping and plugging the water pump inlet or at least use a hose and a metal cap with a clamp on the water pump. DOnt use a rubber cap since they have a tendency to blow out. This part of the system only serves to make heat for the inside of the car so deleting it has no effect.

Lindsey Racing sells a block off plate for the head as well.

I just ran a 5/16 hose from the heater pipe around the block. So far so good. But the real fix would be to block off the pump and block.
My $.99 fix works and I have no overheating issues.