Heh, yeah I never saw the edits.
Ok, the overall impression I'm getting is heading in the right direction, but needs more depth and detail to it - mainly those areas that are just big bland surfaces. For the top of the stern - the textures there don't leave a whole lot of room for interpretation, so I'd just recess and extrude some of the larger panels (the remainder can be done via normal maps), and also bevel the sharp edges to remove the low-poly look. (In fact I'd bevel a fair few more areas with sharp angles for the same reason)
For the underside of the head and neck, I'd go crazy with interesting FS1-esque mechanical greebles inside and around the large flat thing sticking out of the neck. You could turn that into a kind of armour shell rather than the full volume it is now and put piping and stuff inside it:
For the big orange blobby section recessed in the back, I think that whole area could benefit from being recessed further and having organic greebles modelled in. Stuff like lumpy pipes, blobby extrusions and stuff.
With the boxes you're heading in the right direction also, though I would suggest deepening the recess of the orangy brown stuff and making it as rounded as possible. Oh and make the gray square extrusion hatch thing on the bottom of each one stand out more - possibly then recessing that (to make it a rim) and bringing the hatch back out as a cone. Like this:
And finally, for that black middle section between the hatches, I'd turn all that gray area into a nice looking (ie, smoothly shaped) metal armour shell over the orange stuff, like crab armour or similar.
