The bleeders are at the highest point of the caliper...learned that lesson watching a buddy of mine years ago.
The blleding technique used was one man on the bleeder and the other in the jeep. Pump up pressure on the pedal,i open the bleeder and watch the stream.
When the pedal is to the floor i close the bleeder and then the pedal is released. Repeat several times and keep the MC full.
Do you think i need to bleed the master if it was empty at one point during the axle swap?
Several things, your bleeding technique is aerating the brake fluid.
In this order-
Open bleed screw, say down
Helper pushes pedal down fast with enthusiasm and when the pedal is down, says down.
You close bleeder and say up
When the pedal is up, helper says up.
You open bleed screw and say down. Rinse and repeat 4 -6 times per caliper.
If it takes more than two rounds of that, stop and find the problem because all you're doing after that is wasting time and fluid.
If your master ever went dry, remove it and bench bleed it. Get the plastic plugs that fits the ports and install them. Clamp the master in a vise with the ports plugged and the master level. Fill half to three quarters full of brake fluid and start stroking the plunger. Start with short strokes and increase to repeated full strokes until you can only depress the plunger 1/8" to slightly less or so.
Install master back into the rig, remove the plugs one at a time to hook up the lines to the combo valve. No muss, no fuss.
Then do your bleeding again.
A side note- please double check to make sure your bleed screws are oriented correctly. I know you said you checked, but a pedal that goes to the floor after starting the motor is a classic symptom of bleeders on the bottom.