The following is just my opinion.
A soft brake pedal often pointed to air in the system, sometimes this gives a feel of longer travel.
In the days prior to ABS and servo assist you could check this by rapidly pumping the brake pedal, if the pedal went hard and travel reduced and then when left for 5 to 10 minutes went back to a soft pedal again it pointed to air in the system. Even a very small amount of air can make quite a difference on a brake system.The ABS pump itself can be difficult to completely bleed depending on its type and its position in the brake circuits. I do not know what make/type of ABS pump Morgan have used in the Plus 6 ( no parts scematic available to owners ). My experience with motorcycle early ABS pumps was that it took quite a few goes to get the air out of the pump, some even had bleed nipples on the pump itself. There was also a set sequence to bleed the early ABS systems.
In my previous post I mentioned that after our Plus Six M/Cylinder replacement I was not happy with the pedal travel/feel and asked the dealer to look at it again. I am fairly certain they re-bled the system. After their second intervention the brakes on the Plus Six are acceptable and better than pre M/Cylinder change.
Lastly, ref poor handbrake.. Our Plus Six initially had an excellent handbrake, but was noisy from cold in the area of the NSR wheel. The noise sounded like rubbing but gradually stopped after 1 to 2 miles as everything warmed up. The dealer looked at it and reported that the brake pads needed cleaning and light greasing in their retaining area. After this work the brake noise from the NSR wheel area was gone, but the handbrake was lousy, would not hold on a 5 deg incline, so it went back to the dealer and they adjusted it.. Its now back to working well and its not producing noise. So from this I am inclined to think that adjustment on the Plus Six handbrake is borderline and does not take much to either work well or not at all.