Two issues that have plagued me with rear wheel clicking noise. See if either might be your issue...
1. The first time I had the clicking noise I had a rim split in the groove where the cir-clip retains the outer rear wheel bearing behind the right hand grease seal. Wheel would flex a bit every rotation making noise (Really hope this isn't your problem).
Purchased a new rim (came with bearings and spacer). Had no noise with the new rim putting several thousand kilometres on it. While on a trip across Canada on that new rim, I needed to replace my rear tire in Edmonton. While coming home with a couple of thousand kilometres on the new tire and a lot more on the new rim I started getting a rear wheel clicking noise again. When I got home I verified that my rim had no defects so I replaced the wheel bearings and the noise disappeared for around 2000 kilometres.... but came back....
2. This leads to the next phase of the clicking noise problems I've had in the rear wheel that I thought was the result of the rear wheel bearings failing. Did all the usual things. Ruled out bevel box alignment, bearings and gear failure, inspecting and replacing oil same as you. Not the issue. I replaced rear wheel bearings several times only to have the noise come back after a couple thousand kilometres after changes. The only thing that appears to reduce the noise is loosening off the axle nut (it's supposed to be torqued to 81 ft/lbs). I don't like doing this since so many riders don't have noise issues with normal torque on the axle, leaving me with the question, is loosing the axle nut masking the problem. This spring while in Florida, I got the noise back again and started seriously considering checking the cush drive. I have read on the Indian forums that this metallic clicking noise could be attributed to a dry cush drive rubber. One telltale symptom that makes me think this is the problem is a "springing action" (hard to explain) I get when I initially loosen off the axle nut. It's like the cush drive rubber is a bit flexed and springs to a more relaxed state while loosing the axle. Once this happens, the noise is gone until I torque things back up. I just purchased some brand new Natchi C3 wheel bearings and will be pulling the rear wheel again to replace the bearings and check my cush drive interference fit. I'm guessing the amount of torque that's needed might be flexing the cush drive rubber a bit causing it to make this metallic noise. It's weird because the noise goes completely away if I loosen the axle to around 30 ft/lbs but I hate driving it that loose.
Not sure if either of these problems I have had are related to what you are experiencing. Before you replace anything though after verifying you don't have a split bearing bore, try loosening off the axle nut taking careful note to see if you can hear any weird noises. Once loosened a bit, see if the noise disappears. If so, torque it back up to see if it returns. Good luck and keep us posted.