What companies Ball Joints did you use?
Also some people have had trouble getting the old Ball Joints out of the Steering Knuckle. From what I have read mine were not real difficult but not easy to get out either.
When I installed my Ball Joints (I used Lemforder Ball Joints) I also used the C press but I use one from Autozone just to see how it would work but I also had one form Harbor Freight.
I don't recall any need to do any grinding on the C press (and I would not have done that on the Autozone one) and others that used the C press have not said they needed to grind.
What I would have done different is I would have put a washer between the ball joint and the C press because the Lemforder Ball Joint is rounded in the area that the C Press sits on and it wanted to skid off to the side.
See Post 7 for a picture.
http://www.peachparts.com/shopforum/diesel-discussion/393809-1985-300d-front-drivers-popping-knocking.html
The lower portion of the Lemfoder Ball Joints are machined so that then fit easily into the hole that means the sink in at least 1/4th of an inch. The other Ball joints I had URO ones (I did not use them) were fatter in that area and would have been tougher to get in.