I'd carefully restain the stair treads. Know that where there is already/still stain, it'll darken some so wipe that part off immediately. Any rejuvenation product is going to effect the actual color of the wood that isn't stained already. You'll just make that another, different color. So stain them, but wipe the undamaged area first and right away. Let it dry completely before you decide if that area needs a 2nd treatment. Oh, shoot. What did the installer use as a sealer? Because that'll determine if the stain actually changes the OK area. I admit I'm sorry you paid the guy before he took the steps you're taking. It should have been 1) no charge, 2) a no-brainer and 3) a problem a pro wouldn't have created for himself. Someone will probably jump in with better suggestions.

I like strong design usually, but man, that last pic? What do those people do, hop out of bed in the morning, run down the stairs, blow a whistle and yell "Offensive pass interference, the ball will be placed at the spot of the foul. Automatic, first down!"

Yes. Your treads are not Pecan, they're most likely Pine. Pine is well know for being splotchy when stained. A conditioner won't help because it mainly reduces absorption, which limits how dark you can get it. You have two options, go with natural color like your Maple, or water pop the raw wood and then stain. Water popping allows the wood to absorb more stain. It will make the color darker and more uniform, though it could still have blotches.

What a fabulous view! WOW! I am concerned about snow and ice in the winter, given your location and the slope of your driveway. Whatever you choose to do to your driveway and with your garages might need to address that issue. Perhaps using the two end garages and dedicating the center space in front of your middle garage to enable you to turn around or back up without intruding on the roadway would be a better use of that space. Whatever you choose to do there should enable snow removal in the winter, or snow piles. If the entrance to your home is to the right side, I would signal that to visitors by placing a planter, house numbers, a special light, there. A challenging space, but one with a fabulous view!