The solution was to order a new linkage which includes new bearings. Now the suspension is easier to adjust and feels like it should with no creaking.
While emailing back and forth with Santa Cruz's tech department on ways to more easily remove the old bearings, I learned that they are working on a new design that should eliminate this problem altogether. No details yet. I'm looking forward to seeing it. Hopefully it's just a linkage redesign that is retrofittable to current frames.
Meanwhile, here are some tips to ease bearing replacement.
Tip 1: Use the Santa Cruz bearing removal tool with a strip of aluminum wrapped around the pin
Although initially I had more success using a blind bearing puller (black collet tool), the sizes I have are not a great fit for the pivot bearings. Once the tools had worn a bit, they didn't grab very well and pulling the outer race (once the inner race was punched out) was a struggle. So back to the Santa Cruz tool (silver pin and small round part).
The problem with the Santa Cruz tool is keeping the split extractor firmly seated behind the outer race. It helps to wrap the pin with some sheet metal to increase the diameter so it forces apart the split tool. I used aluminum since it was handy, which was good for about 3 bearings.
Tip 2: Use an arbor press
Your local Chinese tool store (Princess Auto, Harbor Freight, Busy Bee, etc.) sells cheap arbor presses. I have a 1-ton although a 2-ton would probably be easier. Well worth the investment, as I've found replacing bearings on my motorcycle.
Here's a simple tool I made on the lathe from a scrap aluminum table leg to press in pivot bearings. Note that it only pushes on the outer race.
Here it is in action on the arbor press. Takes like 5 seconds. No fussing with threaded rods or risk of ovalizing! This is the way to go.