Honey comb varies in thickness and that's how it ends up wavy. If you harvesting it, what does it matter? Leave the best honey combs and harvest the bad ones.
If you want to convert, I'd do it at a time that the bees have time to recover. Late spring or early summer is best, but maybe, if fed, they'd have time to get stocked up for winter now in your climate. What is your climate?
To get them in a lang, I'd do a straightforward cut out, myself. Just cut the brood comb out and tie it into lang frames and havest all the honey and feed the hive until they have a bit of stores to live on. Feed them more before winter after the fall flow is over.