It could be a case of giving too much space too quickly, especially since he was used to being confined. When he poops, is it single poops, or piles? The first is territorial, the second is just laziness. Same with peeing, does it seem like spraying (peeing in a line or scattered), or big puddles?
They are also a relatively new bond, and sometimes it takes a while for litter box habits to improve again after bonding. There can be a temporary increase in marking (like they are staking out their new home as a couple), but then things start to calm down.
In either case, it can help to go back to a kind of litter training boot camp, where you restrict the space to a smaller area (temporarily), like the size of an x-pen. Make sure there is no bedding or anything soft in the pen, and only have hay and litter in the litter box. Soft litter like care-fresh seems really good for litter training. Then when things are looking good, you can slowly start to increase the amount of space they have.
There are some more advanced tips and ideas here: https://binkybunny.com/infocategory/litterbox-training/
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.