You may still have some of the 80lb rock cycling, but as for the transfer it shouldn't cause any more. I recently upgraded from a 55 to a 150 and showed 0 amonia/nitrites through the whole thing. I used new sand, and mostly new water, i tranfered some water back and forth between the 2 tanks for a bit to try and soften the shock to fish/coral.
Dead rock isn't a problem, you may have die off that will cause ammoonia/nitites for a short while, but the rock will re-seed itself and become live rock very quickly. Biggest thing I've learned and been told by most in this hobby, is just take your time. I'd wait a bit before adding fish, test for ammonia/nitrites to see when you tank has properly cycled. Then add stuff nice and easy.
The second chamber is pretty good with the rock imo, look into perhaps making it a refugium one day with some macro algee and a light, but rock itself is most of the filtration in our tanks.
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