I’m not sure how you got this idea but we are flying round trip from Chicago to Brussels. All the other cities will be reached by train. We talked about renting a car but decided to do the train instead.
BTW, thanks for all the great suggestions in the rest of your post. I doubt we will be able to do all of them but there are a lot of intriguing suggestions.
We looked at the Benelux pass but ended up booking the individual legs on the website for Thalys. Since we know what days and times we will want to travel and by booking well in advance, we are saving 50% of what the Benelux pass would have cost. I can see the pass working in some circumstances but the individual tickets will work out fine in this case.
As for the coffee-shops in Amsterdam - although I’m sure we will make a visit or two it isn’t the main reason we are visiting Amsterdam. 