Are there some obvious questions to ask the seller to make sure that I have fully discovered the hidden costs that an older bike is sure to have?
Could you give me an idea on timing to replace items such as: chain, sprockets, various seals, tires, etc., just some of the bigger things that I should be sure to ask so I will not be surprised in 5k miles with a big repair/maintenance bill.
There are two maintenance tasks with the VStroms aside from wear items like tires, chain/sprockets, oil, etc. (the high-mileage bike owner should have receipts for all of the above):
The valves need to be checked and possibly (but not necessarily) adjusted about every 15k miles.
The throttle bodies need to be synchronized at about the same interval to keep the bike running at peak power.
Both of these can be done at a competent shop (if you can find one) for no more than $500. Aside from that, the only thing I've heard of as an issue with the bike is the throttle position sensor, which has failed on a very few bikes. The 650 seems to suffer from this less than the 1000.
Having said all that, I'd go for the lower-mileage, unadorned one. With less than 5k miles, there is almost no chance that the original owner neglected the bike. The only maintenance before 5k is one oil change; and almost everyone gets that first service done. But, even more so, adding accessories and making the bike "your own" is one of the best parts of VStromming. You can make it into anything from a sport-touring street bike to a trail-bashing dirt machine. Or even both...with some compromises.
If you have no budget or desire to add accessories yourself, then get the high-miler. As said above, the bikes are bricks.