antman:

The fuselage being off a little doesn't affect flight trim, only the relationship between the wing and stab (and vertical fin).

Don't go cutting into the stab saddle though, unless you understand the structural engineering back there. If you accidentally weaken the fuselage (such as cutting a longeron) you could lose the tail in flight.

Get the flying surfaces lined up the best you can and ignore the slightly cockeyed fuselage.

Jim