Yes all pistons were pushed back in. One piston popped out (stupidity on my part) but i was able to push it back in.
Before or after cleaning??
Yes, about two reservoirs of fluid. There is no bleed nipple on the master cylinder.
Should i ride it when i get a chance to see if they just need to settle in? Or should i bleed the system again?
I would bleed the system at least another resivour or two. The calipers themselves actually hold a bit of fluid, combined with the lines you may have JUST got it to the point where there's enough in there to work. There's probably still air left in there. If you still have an issue, crack the banjo ever so slightly at the master. Air gets trapped up there and this will help remove it.
If you pushed the pistons back in dirty then there's most likely a bunch of build up on the dust seals.