ok lets start at the top and break it down.
You said its an 02 that means its new enough to have a safety check valve so it doesnt matter if you blead the front or back first. But before you do that I would do a gravel check first. Find a gravel road or parking area get it up to about 8mph 10 at the most and slam the brakes. Get out and check the skid. System working right you should see skips on all 4 tires usually a little less in the rear.
If you dont see skips on one set you know where to start. Bleed that side try again.
On a side note you said that you swapped out the master did you do the drake boster at the same time as when they die braking is worse when the engine is running.
Also your car would have a vacume assisted brakeing system check the hose and connections from the booster to the engine. Also watch for an inline check valve some times they fail giving no vacume boost