First, get the stealership to redo the work right this time and it shouldn't cost you anything more.
If you want to avoid the stealer in the first place, then you can DIY and only pay for brake fluid.
See the attached pages from the FSM.
There is nothing wrong with the Master Cylinder unless you have the dash brake light or ABS light on and have thrown a code.
I've been through this (with multiple caliper changes) and here is what I found works for me to eliminate the spongy pedal.
Ignore the content in the document about the tester.
It's an electric MC pump so start by bleeding with the ignition ON, engine off. The order is somewhere in the document.
Even with a good bleeding you need to finish with step 2a & b (or 5a). If you have previously done a good bleed then skip right to this step. Do the following with the ignition OFF. They say depress the pedal 40 times but here is where they are short on detail. Forty quick on/off cycles is a waste of time. Do 15 or 20 second cycles. Think of how slow air bubbles travel in brake fluid. Depress and hold the brake for 20 seconds, then let go and wait 20 seconds. Imitate the normal braking stroke as if driving. Repeat 40 times. The pedal may bottom out but hold it there. You will feel the pedal go solid at around 20 cycles but don't stop the cycles there. Do 40 cycles. Give yourself 30 minutes to do this.
Repeat as needed over several days and your brake feel will return.
Hope this helps.
I think you're slightly mistaken in the procedure for bleeding the unit. There's a lot of confusion when it comes to the Hydraboost unit, its an odd system most people don't recognize or think about. I'll go into brief detail about the unit itself first.
The Hydraboost unit is a hydraulically assisted and electronically controlled unit. It can be broken down into 3 major sections; the Master Cylinder portion (built like a regular MC), the ABS Module/Solenoid Pack (This contains the brains and electronic solenoids that regulate pressure and perform ABS/VSC Functions when commanded), and the Hydraulic Accumulator Pump & Tank.
The unit is hydraulically assisted instead of vacuum assisted like most traditional systems, unfortunately a large majority of these type of systems I have worked with have a very "spongy" feel to them; I don't know if it is intentional by the engineers or just a byproduct of the extra oomph the hydraulic assistance gives.
That said, the purpose of the "depress the pedal 40 times" is two fold. First its not to build up pressure in the system like you would on a normal system. It is done with the Key OFF to purposefully deplete the system of reserve hydraulic pressure in the accumulator tank. This is a test of the hydraulic assistance section of the Hydraboost unit, it should when the key is turned ON; proceed to run the accumulator pump and build up pressure in the system, this process should take roughly 30-40sec. If the pump only runs for a few seconds, this could indicate you have not depleted the pressure properly, or the pump is weakening. Conversely if the pump continues to run for more than a minute or so, this could indicate a failure and/or leak in the hydraulic system that is bleeding pressure and it is unable to build up proper pressure (this could either mean a reduction in braking assistance or a feel of a "spongy" pedal with little to no actual braking force applied.) The second reason is for the system to refill its reserve so it can start the bleeding process from a "100% hydraulic assisted" state rather than say only half full accumulator tank.
Another thing is when bleeding the Hydraboost unit, it is required that you either use a manual bleeder box (as detailed in the .pdf that was linked, this was used prior to the introduction of the TIS Techstream Factory Scantool) or a factory capable scantool. The reason for this is because the ABS/VSC Solenoid Pack/Module attached on the side of the unit bolts DIRECTLY into the master cylinder portion and controls pressure diverted from the unit. Unlike most vehicles, when using the scantool or manual bleeder box you don't have to "pump & hold" in fact, the scantool tells you to simply press the pedal down once and hold, undo the bleeder valve and let it bleed itself until the brake fluid stream reduces to a slow trickle. The unit will utilize the combination of the accumulator pump & ABS/VSC system to self-evacuate air bubbles trapped inside of the unit and lines.
One other thing to note, is that unlike conventional brake bleeding; where you begin bleeding from the furthest brake caliper from the MC. The bleeding procedure for the Hydraboost starts with the Driver's Front Caliper (IIRC, been a year since I last did it.) The scantool tells you what to do, also another thing of importance, if you are using a manual bleeder box; you must be careful to not cycle the solenoids for more than about 10sec with a 20sec cooldown. The reason for this is because unlike normal use, when using a manual bleeder box you are turning the solenoid on or off, not pulsing it as the ABS/VSC will do naturally.
I'll see if I can get you guys some newer technical documents in regards to the system itself when I get to work this weekend or maybe this upcoming week.
Post Note- It is possible to have a failing portion of the Hydraboost unit and it NOT set a code and/or light on the dash. I had to replace my own unit in my '04 due to a failed o-ring seal inside of the master cylinder unit itself, the symptoms were similar to what the OP is talking about. We determined it was the Hydraboost unit after multiple attempts of bleeding (i.e. 4-6 times in a row and then try again in a day or two), eventually we actually took hose clamps that you would use for say vacuum lines when doing EVAP work or Smog work and clamped off all 4 caliper feed lines and then tested the braking system, we verified that that the MC was at fault when it still had a soft pedal feel even with no where for the fluid to go.
