Paul and Jim are the guru's when it comes to troubleshooting hydroboost units, so I'll let them do their thing and make suggestions regarding the rest of the system. Paul mentioned the
Brake Bleeding 101 on his site which is worth reviewing if you haven't already.
That said, I would start by isolating the front and rear circuits of your system and try to narrow down where your problem lies. I assume that you have confirmed that the master cylinder is fully bench bleed prior to installing it by plugging both outlet ports and making sure that the MC hydraulically locks at minimal travel, but if not, then you should do that before you do anything else. Once the master cylinder has more or less been removed from consideration as the culprit, I would connect the front brake circuit, bleed the hard line at the MC and then each caliper, and check the pedal feel/travel...it should be high and firm. If it's not, then you have an issue in the front circuit as the rear circuit has not been added to the equation yet.
Next, attach the rear circuit and repeat the process. This way you at least be able to begin to narrow down wher the potential problems may be which should help everybody here help you with more specific suggestions.
Most importantly, try not to get too frustrated and be methodical about what you do...whenever I have issues getting a good pedal on a car it's usually because I made an incorrect assumption early on in the process...I could probably start a thread on the subject and I'm sure everybody could contribute something.
Tobin
KORE3