What brand of hydraulics did you use on the first go round? I had a box store brand initially when I did my trans swap and the first master was bad out of the box. Ten years later I decided to change both to AISIN and the master (which was from the same box store) had a decent outer seal leak. The slave cyclinder (yup, also a no-name) had a slow leak for a long time that didn't show itself until I changed it and took it apart. All gunked up and crummy looking inside the piston bore.

I can't promise it'll fix your issue, but there is a reason Toyota has the reputation it does. So it's wise to at least upgrade it all to the stuff that's stamped AISIN in the casting, same as the day it rolled off the floor. I wasn't a believer until I dove in myself. There is a difference from my experience.

Edit: I wanted to ask: did you do a good bench bleed of the master? I've seen it where air gets trapped in the end of the stroke, and the pedal itself may not achieve the master's full stroke, hence leaving a tiny bit of air stuck in it. Bench bleeding is simple (a bit messy) but is damn near fool proof on results.