Dimensioning Difficulties

I am attempting to dimension the few cylinders on this door that are cut with a 15 degree angle on them and then welded to the bent plate. Previously, I had intersected the cylinder and the large plane (plane 2), created a point and then dimensioned to the end of the part. They have dimensioned now to be measured from the center of the cylinder to the intersecting line of plane 2 and plane 3 rather than the edge (plane 3). When I program it on the CAD, the measurement comes out correct. When I actually run it, the cylinder is down and to the right by .100 or so. We have verified using hand tools that it is pretty close to where it should be.

My first plane is off the top of the cylinder. Even that shows off center. If I do not use the CAD drawing and simply check the part, the X dimension is off between .035 and .050 (depending on which cylinder I check). The Zaxis (normally the X (it's the way he created the alignment before I got the cad)) is nearly perfect. Is there a certain order I should be creating my alignment? I'm creating a plane on the small cylinder, leveling it, creating the line, rotating it, and then doing the rest. Is there something else, I'm not considering?

Thanks for any help or suggestions at all.