Good to hear your tuner is working with you.
As for your story, it seems like you know what you're doing. However, coolant temp is not indicative of how warmed up the car is. From a cold start you'll want to idle the car until one bar shows up on the coolant gauge (just a ballpark means of measuring time, per the owner's manual) to allow the oil to circulate a little bit and then drive lightly while keeping the revs under 3 to 3.5k for a solid 10 minutes. After that, your oil and engine should be up to temp and your transmission, differentials, tires, etc. have all also had a chance to warm up.
AFR seems good. MAF calibration being the problem is unlikely, especially if you haven't changed from the stock MAF housing size. Although, if you are using an oiled air intake filter (K&N for example) it's possible that the oil from it has contaminated the MAF sensor and is causing readings to be thrown off. Lack of issues other than the code popping up would lead me to believe it's something after the AFR sensor such as an exhaust leak or bad rear o2 sensor.
On another note, even if there's nothing wrong with the car it would make sense for the situation you described to cause the code since going uphill at 3k would cause the turbo to spool more than normal due to the increased load, and as far as I'm aware, during spool it's technically 'lean' and this could trip the code which has probably has parameters for the rich stock tune, rather than your custom tune which would have different AFRs across the board. I'm no expert on this just thinking out loud lol
for the overspeed code, it seems that it doesn't actually cause a CEL to show, but is rather just stored in the ECU. So I'm not sure if there's a way to tell when it originated. I would still think it was during the dyno tune if the car was run past 7599rpm during a pull. I've read that stock cams and springs are safely good for 7800rpm and it's common for tuners to do this so I wouldn't worry about it. Also I doubt your wife caused it, unless she managed a money shift into first or shifted into 2nd gear past 60mph.
Good luck with your car man, keep us posted. Should be fine really, just gotta get those two pesky codes under control.
Ok, the over speed code makes sense now. It probably wasn't triggered with the other code but at some point earlier without the service engine light turning on. Thanks again for your input. Im definitely still learning.