1) Depends. A custom-painted locomotive can get a higher than "normal" price, but may take longer to sell because the buyer has to appreciate the customization and weathering. Rolling stock, I'm not so sure. Generally when I've sold surplus stuff, I price it to sell because it's taking up shelf space and I'm not looking to get rich. Having said that, I sold some old equipment last fall at a charity auction, and they all took in a considerable amount over their "retail" value. How much of that was the charity aspect vs. appreciating the modeling, I don't know. One thing I can say for certain, if there is a premium above and beyond for weathering, it certainly isn't enough to pay for the time and effort that goes into a good weathering job.
2) Metal wheels definitely have an impact on price, at least from an operational standpoint. I'll pay a few bucks more for a car if it's had its plastic wheels replaced with metal ones. Couplers, I'm not so sure. The buyer would have to be using the same couplers for that to be an added value.
3) Boxes? For me, it makes no difference whether the box is included or not. I'm not buying the box, and it will very likely go to the nearest landfill as soon as the car gets home anyway. Yes, collectors like boxes, but beyond LGB, I don't see a whole lot of collector frenzy in this scale. It may add a few dollars, but that's it, really.
On the whole, though, I've got the same mindset as Richard. I don't buy my trains as an investment. The return I get on my dollar is not financial. When I decide it's time to part with a piece of equipment, I will have gotten my enjoyment out of it, and price it to make it attractive for someone else to appreciate it. I don't weather my stuff to make it more or less attractive down the road, I do it because it makes the model more appealing to my eyes.
Later,
K