I've had the "opportunity" to do this process twice now and I wanted to add my little bit of Blackmagic to the whole bleeding scenario in case it might help anyone. I did the 12 step program and it worked--sort of--got a little bit of movement but never got it to where it was supposed to be so I added a couple of steps that took only a few minutes but worked 100% the first time. That's certainly not to say that the 12-step program is wrong or won't work, but I just had better luck adding basically one additional step (it doesn't look like it from the description, but it's basically just one extra step). Here are my additions:
After rebuilding the pump, I made sure to completely fill the pump cylinder with fluid before closing it up (hint: use the hose from your pressure pot for a nice clean way to fill the cylinder). Personally I think this is THE most important step however you do it.
Reinstall pump but only hook up the line coming from the fluid reservoir.
Connect the pressure pot to the outlet side of the pump (this is easy since it's the same fitting as the T fitting that you would normally be using anyways) and reverse bleed as in the original 12 step program. Also, now is a good time to verify that everything is working which you can do prior to bleeding by giving the pump handle a short pump (beware, it's probably going to shoot fluid everywhere--worth the risk IMHO because at least you can verify the pump is working).
Cap the outlet of the pump using the cap that would normally be blocking the T-fitting (the same plug you would remove to do the regular process) and connect the pressure pot to the normal location. This will allow you to bleed the short section of hose from the pump to the T-fitting. Pump fluid until it's coming out that hose.
While still having a little bit of pressure on the line, hook it back up to the outlet of the pump (will be messy--but so is this entire job).
Now disconnect the pressure pot and replace the cap on the T-fitting.
You should now have a system that functions as intended.