Our system worked very well for us. EtchASketch and I started used my old Fly Creek 2 from the AT. Big Agnes, despite moving their production overseas, still has pretty decent customer support. Whenever something wore out on that thing, they were quick to hook us up. As for quilts, we shared the 32F NEMO Tango Duo, a 2-person down quilt. It did the job well. When the temperature dropped below freezing, we used 15F sleeping bag liners. I can only recommend both of these products, but neither the tent nor the quilt will work with a dog. They simply aren't large enough for two people and a canine.
As for the pads, we both started the trail with REI's Flash pads with R values around 3. We sewed a cap of fabric to hold the pads together at the top and used the quilt's pocket to hold the pads together at the bottom. This system would work well to prevent that "crack" of which you speak. The pads were plenty warm enough the entire hike. More insulated pads will certainly do the job if you can't shake the idea of having a R5 insulation, but the weight difference is all luxury weight.
I had to change pads out in Ashland to a Big Agnes Double Z, and the weight difference was immediately noticeable. Something like 12 oz to 22 oz. Why did I need to switch up? Well, let's start with - I can't recommend REI Flash pads. At some point, REI changed something involving the production of the pads: specifically, whatever holds pad's baffle system in place. After only a few weeks of use, the baffles would collapse creating an irregularly shaped pad. My partner and I went through four Flash pads together (two each; on the AT in 2013, this was never a problem with the older Flash pads). Finally, we gave up and tried different pads altogether. I don't know what Etch went with exactly, but I went the Big Agnes route and never had a problem again with the pad system. I just wish I could have found a lighter, less insulated pad in Ashland than that colossal 22 oz thing. I've also used a Kelty pad since the AT for 80+ nights without any failure on its end. However, none of these pads are the rectangular design you seek. Rectangular pads just add weight without the user benefiting from function. If you are worried about the pads sliding apart, I recommend sewing 1 oz pieces of fabric that you can slide around the pads to hold them together (you'd need two at the most).
I'd also be reluctant to have a dog on any of these pads. Claws, debris tracked into the tent, just flopping down rather than taking care to lie down gently - I think these would all decrease the any pad's life expectancy.