I don't think "once the motor is opened that it never runs the same" is true.
(I never had any problems with my 1991 CRX Si when I replaced the head gasket to clean carbon buildup off pistons tops and inside of head. The engine ran better.)

Assuming you used a good quality click-type torque wrench and torqued the head bolts correctly in stages, there should be no problems with the engine running differently than before.

Other problems to watch out for:
-intake manifold vacuum leaks
-timing belt correctly installed and tensioned
-all electrical connections cleaned and reconnected
-engine retimed correctly

take care,
ChrisS