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Just a guess, but these symphtoms all together are too coincidental. It is pretty typical for failing cam bearings to set a cam position sensor code as the airgap starts to vary. The fact they replaced it and it still sets the code reinforces that possibility. Being a 99 bike there are other things it could be depending on the exact date of manufacture. The real early 99 bikes didn't even have a splined cam gear and they were already either recalled or subject to a service campaign because the bolt that held the gear loosened and the key was sheared. It could be something along these lines, but when you get down to it it's still the same thing.

If the description of the problem is accurate, I think that's what you are looking at. The only thing that makes me wonder is that the guys working on the bike did not even think of the possibility since per your description they had to hear the noise.
The cam bearings also fail more catastrophically, but in early 99 when they first started to fail some bikes ran around for a while with the noise.
Let me know what they come up with, but the smart way is to cover the downside and take it to a dealer. No point paying for it if it turns out to be the cam bearings.

I suppose you could change the oil and filter and look for particles on the drain plug and cut the filter open to look for shavings there. You should get your confirmation.

When they changed the cam sensor they had the cam cavity cover off, it would have taken them 5 minutes to unload the outer chain and see if there was any unusual clearance in the rear cam area. Assuming you told them about the noise. If you did how did they explain it away?
 
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