Jon
Give it a couple of weeks as I have experienced exactly the same issue on other cars and the peddle action improves during that period.
My suspicions are that the cause is the pressure plate self adjustment mechanism not being manually set correctly during the change over.
The pressure plates are dispatched from the manufacturers in a fully adjusted position, but the ratchet mechanism can be dislodged during fitting and you have to wait for the clutch to bed in and self adjust.
The photo's on here show HH manually setting up the clutch with a special tool (all self adjusting clutches use a similar tool), its likely that your garage did not do this check but simply bolted the clutch to the flywheel.
If it has not improved after that time take it back as Honda provide a 1 year warrantly.
Please let us know how you get on
