When everyone switched their pronouns, I installed a subroutine in my brain* that shouts over everything else to provide the correct pronoun. This installation has been fairly successful. Now whenever I think about Hats or Flowers in a way that suggests a pronoun, the subroutine swoops in and, like a poorly altered memory in Harry Potter, fogs over whatever I might have been about to think and booms out "SHE" or "THEY" over top. It's effective, but it's very much a surface adjustment. It's taking while longer for the change to percolate down through the layers of my brain and become a normally integrated part of it.
I also have to import the new genders into different locations. I can think about Hats as female most of the time, but if we go somewhere and do something we haven't since she started transitioning, I find my thoughts defaulting back to the old version of her and I have to 'import' the new version to that place/situation.
Another thing that makes new pronouns hard is when everyone else gets them wrong. I was doing great with Flowers' 'they', but then I went up for a visit and all over the place there were people calling them 'she'. It's so much harder to stick with the correct pronouns when I keep hearing other people using the old ones.
Hats is now out to everyone, but for a while I was playing the pronoun game, where I tried to never have to use a pronoun to refer to her. It was surprisingly easy once I got going. I always thought it would be terribly difficult to avoid pronouns.
*I am not a robot, but I frequently find it helpful to describe myself as though I am one. This is one of the great benefits of studying computer science: It gives you a bunch of cool ways of thinking about how you think.