First time Civic owner, bought an 06 1.8 ES last September. Love the car, impressed with the build quality, just trying to get to the bottom of a notchy gearbox....
Pottsy used to be my nickname at school by the way!
As far as a notchy gearbox two things come straight to mind.
(1) Someone has adjusted the clutch pedal travel to stop the squeek that happens on the pedal. Youll know if this is the case because you will basically have an inch of pedal travel before the car starts to move forward.
(2) Get the gearbox oil changed. The MTF3 oil that Honda use is thinner than 5/30 motor oil and has a life of 70ish thousand miles. IMO its a 30k service item. I changed mine twice and the difference is unbelievable.
There are fixes for both issues in the How To section.
Shameless plug time, https://www.facebook.com/groups/essexhonda/ - The Essex honda group meets a little way down the A12 in Chelmsford monthly; Feel free to join / pop along - I've been putting on a few club stands too, if motorsports is your thing.
With gears; As has already been said - Change the gearbox oil and see how it goes.