well biked

This is false. The cable actuation ratio is a perfect match between your Tiagra rear shifter and your Deore rear derailleur, they should work perfectly together despite the fact that Tiagra is from the road lineup and Deore is from the mountain lineup. Makes absolutely no difference in this case, the cable actuation ratio is the key, and it matches with those parts.

We sell a lot of Auroras at our shop, and the only inherent shifting problem we've found with bikes from the time period of your '09 bike is that the stock shift cable housings are prone to collapse at the ends of the housings prematurely. That's the first thing we check when there's a shifting problem with one of those bikes; you say you've already re-cabled the bike (including new housings), and you've also checked the derailleur hanger alignment. Those would be the two most likely suspects in my mind. One other thing that comes to mind, based on the what you describe and the pedaling uphill out of the saddle when the problem occurs, is that the rear triangle may be flexing enough when you do this to cause the ghost shifting. I've not seen this with an Aurora that I can remember, but it's certainly possible that it could be happening if you're REALLY torquing the drivetrain. The bike has relatively long chainstays, which would be a contributing factor to rear end flex.