Bill -- Uniformity in handgun ammo is probably even more important than in rifle ammo. Seating as straight as possible -- absolutely. Expanding the case and belling the case mouth properly is critical to seating straight. Bell just enough to allow the bullet to start uncanted into the case and see if that improves things.
Having a consistent bullet pull is another factor, and I don't see how you can have a consistent bullet pull with different length cases. Most three-die handgun sets work well, but I've found it is better to crimp in an operation separate from seating.
The primer can also have a good or bad effect on the accuracy of your handgun ammo -- even more so than with most rifle cartridges. If you are using a fairly hot primer like the Win LP (standard and magnum loads), try a somewhat milder primer like the standard Federal 150. If you are using a magnum primer in your 38 and 9mm, try a standard SP primer.
These are just a couple of suggestions which, by necessity, are generic and may not help much, but I doubt if they will hurt.
