I am not sure on how to make sure that the timing is set properly in regards to the engine, but I do know that they make a bolt in timing pointer for the late model cover. I found the bolt in pointer to be a great nuisance and am therefore not going to use it. Most of my problem came from clearance between the pointer and balancer and pointer and water pump. What we are going to do is place a mark on part of the front cover and use that instead of the timing pointer. If you want to try the bolt in pointer, you can get one at a ford dealer for about $10. Hopefully someone else will be able to help out on how to get the correct position.
Dave
Dave