if the back wheel is too far back in the dropouts, will it be harder to manual and bunnyhop? (on 20" BMX) (2003 mirra pro)

do you mean to far back in the drop outs or to far back because the length of the frame is to long?
i think frame length can make it harder along with weight
and if its to far in the dropouts...no

it can effect it, but so slightlt you wouldnt notice. It can make it harder to pedal if you have chain tentioners and crank on them alot.