According the webmaster for the Battlestar wiki, he's spoken to people involved with the show (including the script) and the Vipers on Galactica aren't retconned MkII's but are actually MkIII's. I'm taking that with a pinch of salt seeing as it flies in the face of Adama being established as a MkII pilot during the war.
That's kind of weird. I mean, the cockpit is exactly the same (because it's the same set), almost all of the shape and details are the same, just slightly altered (it's a lot less drastic than differences in the Mark VII or the Zephyr retcon models. Heck, it's less drastic than the difference between the six-foot and four-foot models of the Enterprise-D on Star Trek). And Galactica is obviously the same ship, and it's not even a retcon. We're supposed to believe they ripped off half the guns and walled off three levels of hangar bay.
On the other hand, a borderline-imperceptical model change like that does make me feel better about my headcanon that that sketch from the SDS revival that became the Mark VII was the Mark VI.
They avoided showing it because the effects took forever to finish, and apparently used up so much money that some of the shots are lifted straight from other BSG products.
That's how it seemed at first. IIRC, set photos of them shooting were leaked around February, 2011. There was silence about progress until November, 2011, when Doug Drexler said B&C had just wrapped
. Bear McCreary revealed he was scoring it sometime within the next two months, and by February of this year, he said he'd finished recording. Music is pretty much the last thing done, so at that point, it was ready to go. That was confirmed in March, when the leaked teaser came out, showing a bunch of completed scenes.
So, yeah, they've been sitting on this for at least eight months since it was ready to air. Possibly as much as a year, since Bear reported it as something he was now allowed to announce, not something that had just happened, so it might've really been finished
-finished, editing, sound, music, the whole shebang, when Drexler made that blog post.
The interesting part is the lengthy gap between photography and wrapping post. The apparent answer was that B&C was biting off a lot more than they could chew and it took almost a whole year to do all the 3D work. That's ruled out by the CGSociety article on B&C
which mentions that post took up five months (which, yes, is a lot, but it's a lot less than the eight months Drexler's post suggested, and a hell of a lot less than the two year total between shooting and release). My guess is that there were delays during production caused by Universal and SyFy constantly going back and forth on if it was a webseries, if it was a movie, if it was a pilot, if it was cancelled...
As for the stock footage, so far the only incidences of that were in the opening narration, and there wasn't any stock footage beyond that in any of the trailers. My suspicion is that it was added in fairly last-minute, mostly stock footage and a couple of new or refurbished shots that could be banged out quickly. I'd bet the Cylon carrying the kid was originally shot for the montage/trailer in the Caprica finale, and cut out or never finished.