For dual bleed screws on brake caliper...
1) Bleed mostly from top screw to eliminate air.
2) Bleed a little more from bottom screw to eliminate debris.
I think you should wait till the engine is in the car and running.
Due to physics...
Pressure is defined by mass divided by area - i.e. pounds per square inch.
You have effectively increased the "area" side of the equation due to the larger brake master cylinder bore.
Now you have spread pressure over a larger area...
Thus, the feedback pressure is going to be less back to your feet - i.e. softer pedal feel.
We need the brake booster to be operating to see how effective the whole system is under working conditions.
I think you're just wasting brake fluid and labor at this point.
-Ted