I am in the process of putting my S4 components on an S5 block and I am going to change the front covers now, but I've been reading about the torrington bearings causing problems, I can't find any good instructions on front cover swaps and I don't want to mess anything up.
Should I change covers with the engine in the car, or out? I suppose it's a good thing that I couldn't get the e-shaft bolt off, as I had not read about the bearing probs untill now

 

If you're going to pull the engine, then do it out of the car. But if not, it can be done in the car. Just pay attention to the bearings. Easiest eay to hold them in place is to wedge the clutch pedal down (make sure your hydraulics are in good shape). For bolt removal, the only way to go is an impact wrench.

 

it's already out, mazdatrix, or somewhere I read, said to place the engine verticaly with the flywheel down, is that the best way to go?

 

This is from the Mazdatrix website:

http://www.mazdatrix.com/faq/pulley.htm

 

Yes, make sure that the engine is flywheel down and don/t move it until the job is done. the reason being is that the bearings can slip if you have the engine horizontal and then when you tighten the bolt, you mash the bearings!!!!