you can optimise the set up of your bike all you like, but without the ability to run different maps for the front and rear cylinders it will always be a compromise. it's worth noting that you didn't feel a problem riding it, only from a physical inspection of the parts.it's not something to worry about as the ecu's have had the ability to map seperately since about 93 (p8 comp.) and the factory didn't start to utilise it until the testastretta's (i think!).Going from your current set up, at it's best, to a differential map set up, at it's best, i'd be very surprised if you noticed any difference at all.
cheers, paul.