Welcome aboard, ENGAKATS!

Yep, the stock gunsights are particularly off.
Only thing you can do is editing the pitch of the guns inside the aircraft's xdp file.
To do so browse to your CFS3 installation path.
You'll find a folder "aircraft" there which holds all the, err, aicrafts.
Inside the various planes you'll find a file "myplane.xdp" for instance.
You can open and edit it using a text editor such as Notepad.
Right at the top of this files are the gun station definitions.
towards the end of each line you'll find something like
Pitch=".1489"
Change this to 1.0 as a starting point. you may want to dabble a bit with the values.
Once saved delete the file with extension bdp inside the aircraft subfolder or the changes won't happen.
This one will get newly created when you run CFS3 the next time.
Just note changing the xdp will take away your ability to fly online as it will give you missmatch errors.
Other than that get as many 3rd party planes as you can as they have their pitch usually tuned correctly.
good sites are here at Simviation, http://www.groundcrewdesign.com or http://www.avhistory.org/ for instance
Oh, and of course before you change anything to your game make shure to install the 3.1 and 3.1a patch available at http://www.microsoft.com/games/combatfs3/
Once patched get the no CD utility to save your CD from scratches
You can find it here at Simviation right at the top of this site:
http://www.simviation.com/cfs3utilities1.htm

I just tried it.

I changed the pitch to 0.85 from 0.49something. now on the vertical axis is on the same level with the centre of the cross.

but it's still out of the cross, to the right of it. or, to say it better, the cross looks like it goes more to the left.

I tried to find another value similar to pitch but now in order to change the horizontal value, but I couldn't.

any more suggestions??

The gunsight is out of line??? Weird, my one was absolutely perfect when i got the game....