Only changed the pads not rotors. I did sand the rotors with a hand held
Bosch detail sander and there was an improvement similar (but not as
pronounced) to the improvement when the rotors have a light coating of
overnight rust on them.
I think I agree that it is something not moving as it should and given
what was done (i.e. pads pushed back in callipers) I think that it would
be prudent to have the calliper bores and pistons cleaned to see if that
makes any difference.

The one thing that I find odd is that when the car went back in to the
dealers the first time (after a couple of days) they found air in the
system and charged me another £30 (on top of the £200+ for the pads being
fitted) for removing it. When I asked why the charge when they had just
fitted pads and should have bled the system then, the dealership got very
defensive and quite hostile when I refused to pay and would not give me my
keys back until I paid the money. They insisted that they could not have
got air in the system and it must have been something that I had done to
the car which was not true, I only started working on the car when I had
exhausted every avenue of getting the Franchise to get my brakes working
the same way as they were when the car came in to have the new pads
fitted.
The total defensiveness of the dealer made me think that they had done
something to the car that they were not going to admit to and then 6
months down the line tell me that I need a new master cylinder or a new
servo. I have used this dealership for the last 9 years or so and have
only had problems with them when the local owned franchise was taken over
by a much larger national franchise also I have found out from on of the
guys there who worked on the service desk and has since left the place
that most of the mechanics who had been there 15 years+ had left the place
and gone working for Jaguar, Ford, Volvo, Mazda etc so something there is
rotten and I feel that they have "economical" with the truth over what has
happened to my car.
All I want now is to get my Civic working properly at whatever the cost
and I will NEVER be using that franchise again, problem is that they have
taken over nearly all of the local owned and family owned Honda garages
for miles around leaving me no option but to drive miles to get to a
dealer that isn't owned by this particular franchise.
Sorry about the soapbox rant but I needed to get it off my chest and I
still believe that they have screwed up something major and expensive and
are keeping quiet about it.
I still favour that they have knobbed the master cylinder in some way
shape or form when they pushed the fluid back into it as opposed to
cracking the bleed nipples off and pushing the fluid out that way.
Is there any way of testing the master cylinder or servo to get
quantifiable figures??

All the help is much appreciated and I will get to the bottom of this,
eventually.