Question #1...Did you check to see if you need to change the shims?
If yes,
Question #2...Were you able to determine if you have front or back focus?
Instructions here: Focusing Screen--How to adjust focusing screen--
If back focus, you add additional thickness to the stock shim (if any) between the screen and the pentaprism.
If front focus, you remove the existing shim and replace it with thinner stock. On the K-r, there is no additional retaining clip for the shim.
Edit: Forgive me for not reading your original inquiry carefully. If the stock shim yields accurate focus, simply put it back in and be happy. If not, reference the struck-out text above. I suggest that you test it (camera on tripod) against a nice, high contrast target with a strong vertical line. Test at about 20x the lens focal length and use a lens originally designed for manual focus, if you have one. A longer focus throw is easier to work with.
Steve
---------- Post added 10-06-14 at 04:09 PM ----------
You may also want to review the instructions on the KatzEye site. They have excellent photos and also include detailed information regarding the shim.
http://www.katzeyeoptics.com/files/install6.pdf
You should not have to remove the stock shim (if any) unless there is a front focus problem. I don't know why focusingscreen.com includes that step, since they have you put it right back in.
If you need additional plastic shims, contact focusingscreen.com. Pentax no longer sells these parts directly to consumers.
Steve
(...apologies to Rachael Katz...)