First, when flushing an old dirty brake system, flush the system BEFORE you install the new components, calipers, wheel cylinders etc... Other wise if you install the parts before you flush it, the crud will go into the new components.
Second since brake fluid is hygroscopic and absorbs water, if the fluid has been in the lines more than a few years the lines have probably started to corrode internally. Like an old radiator or heater hose, you won't know if it is bad until it fails. Brake lines are so inexpensive and the brake system is The most important system on your car. It just make s sense to do it safely and do it right. For just a few hundred bucks total you can replace all hard and soft lines on your brake system.
To find your restriction, disconnect the lines from the master and the rear wheel cylinders and blow some compressed air from the master cylinder to the rear lines. If it blows clear, the problem is forward. If not you can disconnect one rear line at a time starting with the flex line at the differential.
When bleeding, Always start at the farthest point from the master ( Rebuilt master cylinders are notoriously unreliable, I always use new) and work toward the master cylinder. If you don't have a bleeder and are doing it manually by pumping the pedal, put some sort of block, 2 by 4 etc.. under the pedal between the floor. This will keep you from bottoming out the master cylinder piston when pumping the pedal. Bottoming the piston can/will cause internal damage to the M/C.
Always use fluid from a new/ sealed bottle. Once you open a bottle of DOT 3 fluid, it starts to absorb moisture which degrades the temperature rating of the fluid. If you make bake fluid changing part of your vehicles regular maintenance procedure like oil, coolant, transmission fluid changes you will enjoy many more years of trouble free service.
For those that didn't drive in the sixties or before, Fluid changes of all types were a constant maintenance item. Cars burned/leaked a lot of oil.
In the "old days" there were always displays/racks of oil right on the pump islands because it wasn't unusual to check and top off the oil at every fuel fill up. Todays cars are virtually consumer maintenance free with very little being user serviceable. The old lubricants and various fluid/grease seals were not as refined or made from the improved manufacturing/synthetics that we have today and were therefore more prone to rapid wear and premature contamination. Oil and transmission/gear oil changes were frequent. A was wheel bearing repacking. Most of these service were done 2-3 times a year and cars were riven much fewer miles than today.
Regardless of what the current manufacturers tell you, there are no "lifetime" fluids. We just live in a throw away society and are not encouraged to maintain anything. Just replace it if you have a problem is the attitude today.
Take care of your car and it will take care of you. Make sure to have the Factory Service Manual for your car and read/use it. M No magic to servicing your car.