What is wrong with my car?

I currently own a 2000 Dodge Neon. It's almost at 100,000 miles and I got it Spring of
2012 at around 75,000 miles. I was coming home from college for the summer in 2013
and I have reason to believe I hit something going 65 mph. I heard a very loud *POP*
sound and ever since, if I drive between 65 and 70 mph for too long, my engine will
start knocking on the driver's side even though whatever it was I drove over was on
the passenger's side. It was much more prominent over the summer when I had the
AC on and it's not doing it as much now that it's getting colder. I had a mechanic
check it out and of course there was no knocking to be heard. It knocks loudly when I
floor it as when the transmission is kicked into high gear. I talked to my boyfriend's
dad about who knows a lot about cars and he reassured me it wasn't a rod of any kind.
I have yet to change my oil from late summer which I will do sometime soon and the
spark plugs are like new since I changed them over the summer as well.The last time I
checked my transmission fluid, the stick said it was low but I have yet to actually refill
it.Could it be my transmission fluid just needs flushed and refilled? Is it possible my
AC is just going bad? Is it because my car is misaligned that it starts knocking at high
speeds? As said before, it doesn't seem to knock under 65 mph. When it does knock,
I let up off the pedal and the knocking stops only to have it return almost 20-30
minutes later of driving.