It might not look the best and some of the dimensions seem a bit off (such as the side pods with the landing gear, they look a bit too flat but if you were to add another row of blocks it would look too tall), but after looking at some reference photos and considering the limitations of this game it is a very good build.
As for the pods being upside down, the only way in the current build is to have to pod dock to the underside of the upper plate of an adapter which is then docked to the Eagle. It would make the interiors of the pods match the orientation of the main ship and the doors would also line up. At this scale the results would look much worse. After playing around with the DEV build of StarMade I'm sure this design would work much better with the new docking system. (Davetheon, you can start making 'right-side-up' versions of your pods then saving the blueprints so when the update happens all you would need to do is add the correct 'docking' blocks.)
For the problem of 'collision' at the fore and aft of the pods, I would recommend removing the 'collars' from those pods and adding a ring of plex door blocks around the doors on the Eagle, then add an activation module nect to the mid-line docking point, link that activation module to the plex door rings. When pod is docked the rings 'close' eliminating the gap. When pod is detached the rings 'open' giving a one block clearance.
Sadly you're right about the scale choking the artistry of the model. I updated the intro page above with scale comparison images if you're interested. I was first and foremost wanting something that was a functional representation of the Eagle concept in game terms and where form conflicted with it function won out. For a much nicer and more accurate artistic rendering check out BinHawkins2013's ERTL Eagle.