Was it changing gears difficult before the brake pipe change or did it start after it?
If before it was changing gears easily and after not it's indeed possible there's air in the system, simply bleed it and you should be fine.
If that doesn't fix it (and it was already there before the brake pipe change) there's also a way to adjust the gear select cable.
Select third gear.
Remove the gearshift cables cover.
Release the selector cable adjuster locking insert
Depending on whether you're car is from before 08/2003 or 08/2003 onwards push or pull the orange knob on the selecter cable.
Install the gearshift cables cover.
Wow, what a story. That air can come in but no fluid out i can confirm that. Not with the Ford but with my Mercedes, Couldn't get the rear brakes bled with just pumping the brake pedal. Not even in the garage with a vacuumtool.
Then i build my own pressure bleed tool and then it worked in 5 seconds.
I recently renewed my brakefluid and also the clutch fluid. With a pressure tool it's 2 minutes work and your pedal will stay hard. (Made a how to in the Fusion how to section)
I don't like to bleed the brakes (clutch doesn't matter) by pumping the brake pedal, it can damage the internals of the masterbrake cilinder because you push it further in as normal. With the clutch pedal that isn't the case, you Always push it in completely.
Good idea to clean everything, that way you can detect leakages much easier instead of seeing old leakages.
Hope it solved now!
Just go to this page: http://ford.workshop-manuals.com/Fusion_2002.75_06.2002/index.php?id=611
it's the whole workshop manual, index on the left side, very good site if you want to do something on you're car.
You can see how to release the quick coupling, just pull out the clip a little and that should be it.
Glad you got it sorted out!