Remove a clip and press the cap against the opposite clip. This will move the few thousands of clearance away from the clip groove. Reinstall the clip and smack the other yoke toward the reinstalled clip. Repeat on each cap. If this doesn't help, reinstall your original clips and try again, As long as they seat tightly they'll be OK.
The stiffness is from a cross end being in tight contact with the inside end of the cap. These are hardened, finished surfaces that function as thrust bearing surfaces in operation. In operation the U joint self centers. If you install the assembly as is, it will most likely loosen up on its own. If you're concerned, run it on muffs for a few minutes, pull the drive and check for stiffness. My bet is it will be loose.