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Oh man, a lot of good questions.
To stop the popups, type /grss noloot. This will disable the popups, but the items themselves will continue to be recorded.
At this time, unfortunately, the waitlist prompts still need to be approved, though that could be a useful option for the future.
To disable the wipe detection, type /grss nowipe.
Finally, for the epic gem stuff, currently the only exceptions to the items have to be manually entered by name into the mod. Disabling the item popups will at least stop the popups, and then you can just make sure to uncheck the box when uploading.
Also, I recommend typing /grss reset, rather than deleting the data file after uploading, otherwise your saved settings will be lost (the noloot, and noitem settings).
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It's all in the reflexes.