Wow, okay, where to start...

First off, I'm glad someone was paying more attention than me. For the life of me, I could not remember the length I'd come up with. Thanks Major D!
Now onto your suggestions... The warp nacelles are connected that way because I like the way the profile looks. I was a little worried about the way they are connected, as well, especially when it comes to structural integrity at warp speeds. But I figure that if Starfleet could build this thing, then they could probably take care of those issues.
The two aft shuttlebays I think you are referring to are actually doors into the cargo bay. Its meant to be one large cargo bay, perhaps segmented into different sections. I'll develop that more later. Right now, I'm still finishing the last little design details.
I'm guessing by landing gear you mean the hatches on the bottom of the ship. The two round ones aft of the docking bay doors are the warp core ejection hatches (two warp cores, one for each Nacelle, which are like two Nacelles in one.) The rectangular ones are hatches for the weapon turrets. The spec sheets are in a previous post, and have a few made-up details about the ship.
As for the impulse engines, I wanted something reminiscent of the thrusters on the back of the "real" Galactica, but still fit in with the trek tech. Low and behold, I was inspired by the impulse engines on the NX-01. They look blue like the Galactica's thrusters, but are impulse engines from Trek.
As far as the fighters go, that idea hadn't really crossed my mind. You just opened up some more options to me. I'll think about it while I'm working on the vipers. Thanks!