I've been fishing Pipestone since 1960. Yeah, I was a kid with my Dad and we have a place on Clearwater. Personally, I think your best chance at a Musky would be on Clearwater. If you work Clearwater for five days and have some experience you will catch a Musky. Pipestone can be a bit daunting because there is so much water - about 25 miles worth from end to end including going into Schistose lake off the far end of Pipestone, versus Clearwater's eight miles.
I've had my best success on the Clearwater / Pipestone chain using neutral and natural color baits. Brightly colored lures haven't produced as well for me. If you do go to Pipestone, try to limit your fishing to a few specific areas. I'd start with the Northwest Bay of Pipestone. It is shallower and there are more island clusters here to focus on. Alternatively, the first three miles after you cross into Pipestone from Clearwater before the lake opens up should produce some fish.
Musky season opens the third Saturday in June, so the weather by then should be pretty nice. If you go, send us photos of your fish!