Well, visual integration is usually dependant on how the eye travels over the object. In the case of your ship, there is a break between the cannons and the the lines on the ship. As your eyes travel along the edges of the panels and the silhouette each line sort of leads into the other. There's a continuity or a visual momentum. If there's a big break and nothing leading up to an object, then it feels isolated from the rest of the model. Sort of like it was just stuck on. An example of this are the arms on the body. The way they're set up they lead into the shoulder and the pectoral muscles. They feel attached. Now, if you cut them off and stuck them back on somewhere else, there wouldn't be that lead up to it. They wouldn't feel like they belong.
Here's an example of what I meant by integration. I've shifted the top ones to the edge so that they streamline into the main body and dropped the panel to encompass the lower guns.
A more drastic version is this next one. Instead of moving the guns, I've moved the edge inwards. This method changes the character of the model quite a bit.
FreeSpaceFreak's suggestions could all work as well, provided you consider how the eye moves over the armour plates or the extrusions.
I also agree about the older version looking more integrated then the rounded portals. Another thing that should be of concern is whether an element is repeated anywhere on the model. In your older version, the hexagonal ports were echoed in the plating found all over the ship. This tied your model together visually. Think of it like having a unified colour palette, but in form rather than colour.
Hope this helped. It's a great ship, and I'd love to see it finished.
