A thicker rubber pad will allow the pedal to cover it's full travel with less 'leg input' but how thick does it need to be ? Any device fitted to the pedal will have to be securely fixed to prevent it slipping and fouling the brake pedal. There's also the possibility of your foot fouling the underside of the dashboard panel if it's too thick ?

Can the seat not be adjusted forward or lowered to counteract the limited leg mobility ? If you try adjusting the pedal by mechanical means it could cause premature clutch wear so moving the seat is the best and safest solution.

If the seat is as far forward as it'll go, how about one of them orthopaedic cushions fitted to the backrest so your wife will be seated slightly further forward ?

Is there anyway of reducing the clutch pedal travel to engage or disengage as my wife has had a knee operation which limits her mobility. My garage says that it is hydraulically operated. I thought that there may be a a thicker rubber pad that can be fitted and purchased

If your wife's mobility is permanently (rather than temporarily) restricted I would seriously consider changing your car for an automatic model.

When I changed my wife's car 2 years ago I had a similar consideration (limited movement in her left foot not requiring an operation) and we've never looked back. It's so relaxing in all driving conditions but particularly around town / city driving. It's even more perfect when combined with an EPB - makes perfect sense in an automatic.

I wouldn't go back to a manual by choice now and neither would my wife.