My LBS guy came back from Costa Rica and put my bike (the 5000) together this past weekend. I went yesterday so he could fine tune the fit and give me some practice using the clipless pedals. Unfortunately, I couldn't take it home because it was pouring. So I'm still waiting to get on it. This weekend had better be sunny!
To answer your questions:
I'm not going to swap out anything until I ride it for a couple of weeks. Then I'll have a better idea of what feels good and what doesn't. I don't know enough yet to make that kind of decision without trying it out first. I have a strong suspician that the saddle will need to go, so I'm also interested in knowing what mweber did about her saddle - or anyone else who has that same saddle.
I'm barely 5 feet tall with a 70 cm inseam. I can stand comfortably over the top tube with about an inch of clearance and with my feet flat on the floor; although with padded shorts, I think it may be less than an inch. I cannot sit on the saddle and put my feet flat on the floor. Tippy toes there, but I don't think that's a concern because I'm used to getting off my other bike, which is way too high for me, when I come to lights. However, I didn't have clipless pedals before, so I expect to be challenged in that respect. I'm trying to decide where I should practice before I go for a real ride.
We set the saddle and handlebars to be pretty much even in height, although my LBS guy thought I could handle the handlebars a little lower - more racy. I decided to keep it even for a few weeks to see how easy, or not, it is for my body to get used to being in road bike position.
I hope this helps. I'd love to know what others have done as well.