You probably have your lines from the pump reversed. Middle line goes to the left side (looking from front) bottom line goes to the right side (looking from front). It doesn't matter which you have hooked to your siphon or your pump, as long as it's hooked to the right spot.
So, what you have is correct... assuming the line from the hull to the exhaust manifold is going to the Left (looking from the front) since you have the pump connected in the middle in the back. See image below. If in doubt, use an airhose.
Other possible problems...
You have a kinked cooling hose.
You have the gasket completely sealing the junction (Ie. the exhaust manifold gasket doesn't have holes to let water into the head)
You have too much corrosion blocking it.
Pump sucks and isn't pushing water.
No matter how you hook it up, water will flow. You could hook it up backwards and the water would still come out the pisser. It'd run like ******** and probably over heat, but the point is, as long as it can go in 1 spot and out the next it will come out the pisser. It's either being blocked or it's not getting into the lines (pump isn't working or you have wrong line through hull).