The other thing you might check is the stem on the bike. (It's the piece that attaches the handlebars to the upright.) They can be different lengths and some angle up. This is all part of bike fit. You can have a bike fit at your LBS or keep experimenting on your own.
I bought a used Bike Friday that I thought fit pretty well when I test rode it. After a long ride, both my hands and me seat hurt. I went and bought an adjustable stem. Imagined where my hands would want to be (in the air). I adjusted the stem to that position. No more pain. I also needed a new saddle. The tilt of the saddle is also very important. If it tips too far forward, you put too much weight on your hands and they hurt.
I don't know how many bike stores will actually try different seats on your bike, but I had an idea that you could try a bunch of bikes (not yours) at the bike store which have different saddles to see which one feels better. The really soft big ones are not good for long rides and you cannot feel your 'sit bones'. The really hard skinny ones feel uncomfortable to me from the minute I sit on them. Personally, I fit on the WSD (women's specific design) Specialized Dolce seat.
2007 Ruby Comp/Specialized Dolce
2004 Bike Friday Crusoe/Specialized Dolce