I'm in the exact same boat. I dropped barbell squats totally for now until I get some more strength/flexibility in my hips and ankles.
I started out doing Overhead sqauts with just a broomstick, and worked up to the ol bar. About 2-3 times a week I'll do 2 warm up sets of OH squats with the broomstick then 2-3 sets with the ol bar. After that I'll do 4-6 sets of Kettlebell front squats, and I've been getting really deep on them. I can feel my ankles aching just a tad from exceeding the limited range of motion that they've been used to for the last couple of years post injuries. But it's working for me, and maybe in another month or two I'll start doing some regular squats again.