I put e85 in my dad's 2003 Subaru Baja, please help..

my dad has been letting me borrow his car and I
did not know that I wasn't allowed to put e85 in the
car I was putting e85 in it for over two weeks
before I noticed the change and the malfunctions..
it's been over a month now of me putting the
correct gas in but recently the car is having trouble
shifting into next gear when I need to accelerate or
when I'm going up a hill but doesn't want to move
into that next gear could this be due to the e85 or
is this a completely different issue?  it reminds me
of The Little engine That could just trying to chug
chug chug along.