if i understand correctly
the engine is running correctly
but the car is going backwards
right?

if so, there are only a couple of things
i can think of to cause that

one - the engine was removed
and replaced backwards
so that in spins the gears backwards
pretty unlikely i know

two - on some trucks
like the t-maxx
if the diffs are removed
and reinstalled upside down
the truck will run backwards

three - the reduction gears
were removed
and replaced the wrong way

a picture or two of the
vehicle may help us
help you