Boy, so many good responses and ideas here already and I think you are on the right track. Start with making sure you have comfortable pants/shorts. If using lycra shorts, they should fit (and I see you are good there now.) In winter, I can commute to work in jeans but in summer when it's hot I sweat and need to wear shorts with chamois to keep from chaffing.
You had an initial fit to the bike, so that gave you a good starting point.
Your stock saddle may be part of the problem (yea I agree with the others here on that one). The stock Bontrager saddles are too padded and not too comfy (they are not the much better Inform-and even those in WSD are way too padded IMO). More padding does not always mean more comfort, is is usually just the opposite. You don't want to sink in like on an old couch. That's not support.
Did you try your old saddle on the new bike yet?
Another thing to be conscious of when riding: how you sit. On most flat-bar type bikes, you are more upright, which puts you on the sit-bones and not the soft tissue. When put on a road bike with drop bars, it is easy to make the mistake of rolling the hips back to get bent down to reach the bars, basically flat back and levering down as opposed to sitting like on the flat-bar bike and bending at the lower back. This takes some getting used to, and good core strength to support yourself on the bones and not collapse your weight on to your hands. Rolling the hips back puts your soft parts on the saddle and can cause burning/chaffing/numbness.
Tzvia- rollin' slow...
Specialized Ruby Expert/mens Bontrager Inform RXL
Specialized SWorks Safire/mens Bontrager Inform RL
Giant Anthem-W XT-XTR/mens Bontrager Inform RXL
Fuji Newest 3 commuter/mens Bontrager Inform RL
Novara E.T.A commuter/mens Bontrager Inform RL