From where you're at now, this is what I would do:
1. Take out the wheel and pads.
2. Intentionally overextend the pistons with the lever. Clean them and the whole caliper thoroughly with alcohol.
3. Swab Royal Blood onto the clean pistons, then push them back in. Repeat several times until they seem to be moving as freely as they're going to.
4. Put in a bleed block (I always use a 10mm allen t-handle for Magura because it's way stiffer than the official yellow plastic one and is the same dimension. The stiffness is good because the way the official ones compress when you test at the lever after the bleed can make troubleshooting difficult). Bleed the brake.
5. If uneven retraction issues continue, live with it or replace the caliper.
Also, having the mounts properly faced will only help reduce these issues, even if it was good enough when the caliper was new and working perfectly.