I ended up taking out the filter thingy (wasn't too hard after all), and used a syringe to take out a bit of the fluid and temp store it. that was the missing "ingredient" to getting the pistons back in. I used the tool from AutoZone ($8) and it was worth it. Made the job easier.
Got all 4 corners done, started her up and the pedal went to the floor. Pump it one time and it was "back to normal". Bedded them a bit and then gave her a bath
The hardest part of the whole job was gathering all the tools needed!
EDIT: p.s., the FLAPS doesn't carry the cabin air filter, it's a special order item... bah