I also just upgraded the automatic hubs on my 4x4 to Warn manual hubs today (yay me! ) so I figured I'd try to weigh in. Do you still have the retaining/snap ring and washer for the hubs or is that picture you posted pretty much how it is in there? You can kind of see it in the photo you posted but if you run your finger down the splines you can feel a place where there's a groove that goes all around the spindle. Right in there is where your snap ring and washer (Thrust washer?) would go.

When I switched over to manual hubs the instructions in a roundabout way stated to keep those parts. The directions provided by Warn were also absolutely awful in every way so I turned to the internet to see how necessary reusing these parts were. What I found was that they may or may *not* be necessary but having them installed would reduce "play" in the system.

If what you did was an auto hub to manual conversion and you still have the old parts it's worth a shot to try to throw 'em in and see if there's a difference. When did the noises start? I only have 4 miles on my new hubs so take whatever I said with a grain of salt