Well, as I said, you are running a 4.0L (it looks like) and I have a 5.0L, so setting the timing is different for each engine. But, from what I can see, the setup is the same.
Basically, the 2 key components in the setup are the body of the Camshaft Position Sensor (The part you bolt down) and the Sensor itself. What the Camshaft Alignment Tool does is set the vane (the half moon shaped protrusion in the rotating part of the housing) to the proper position it should be in relative to the Sensor at TDC.
All you should have to do is bring the engine up to TDC on the Compressions Stroke, install the Camshaft Position Sensor Housing WITH the Alignment tool installed and properly engaging the vane. You then bolt down the housing with the Alignment tool still installed. This locks the housing in place and ensures that the Sensor will be set properly. Now you just remove the alingment tool and install the sensor. I may be wrong, but the 60* of center line thing shouldn't affect the sensor at all, but is probably set that way for clearance of belts and the wiring harness... the only things that set the timing are the housing and is relation to the Sensor which should have no bearing on how it is oriented into the block.
One key issue. You need to make sure you are TDC of the COMPRESSION stroke. If you are at TDC of the Exhaust Stroke, your timing, fuel, etc... will be 180* off and your engine will run like trash because it will be injecting fuel and firing the plugs at the wrong time.
As I asked before though, are you using the tool that came with your CMP, or the one you purchased after the fact? I believe if you got one for a 5.0L instead of a 4.0L, it would still install properly, but it may not set the timing properly (I've never compared the 4.0L to 5.0L before).