dont mash on the pedal if the pads are new - they need some time to burnish. When not burnished it may give a spongy pedal as the brake pads have not bedded.
I also never close any bleed nipples when bleeding the brakes on one man system without pressure, if your catch reservoir is above the nipple level then you dont need to close it as the weight of the liquid in the bleed discharge pipe ensures no air can be sucked back.
It is vital that the pedal be pumped slowly.
Now heres a bit of "somewhat" bad news - if you suspect the MC has trapped air.
If at any point of time the master cylinder went dry - its loaded with air which wont bleed unless you bleed it individually first, Its very easy - you need some cut up brake connections and some transparent bleed pipe.
remove all the brake pressure pipes - and connect your junk fittings, push the clear pipes over them and dip them all into the brake fluid reservoir on the cylinder, slowly pump the pedal half stroke each time and wait about 2 seconds between pumps - make sure you release the pedal completely on each pump. The air bubbles will be seen in the pipes and when the fluid goes clear - the MC is ready for service.
connect all your hardware back and bleed the wheel slave units.