2005 baja sport timing belt issue

[bajaroy]

Me and my father who used to be a mechanic put a new timing belt on . all the marks lined up as they should . we turned it over by hand first to make sure there were no problems . then i started it quick to make sure before i put the harmonic balancer back on. and it runs like it is miss firing . with or with out the balancer . is there something we are missing