I am trying to upload my code onto my uno, but I have noticed that it cannot find the correct port, and when plugging the cord into my computer, the lights do not turn on. I have noticed it only does this with the motor shield attached to the uno. How can I fix this?
Sounds like the shield uses pins allocated to the communications.
But without knowing which motor shield (there are lots) and only being able to guess at what your sketch contains thats about the best I can come up with right now.
The motor shield I have is a cheap one I found on amazon.
Ok so its a sainsmart which is almost identical to the earlier Adafruit ones seemingly.
Its based on the V1 of the shield listed HERE
There is also some good reference material HERE
Looks like it doesn't use the D0 or D1 so coms should be OK
As should A0 - 5
The manual is HERE btw.
There is mention of the jumper and on some versions a track pad that may have to be cut so maybe research that aspect in case the way you are powering it up is an issue ?
Otherwise there doesn't seem to be a reason for what you are seeing.
It's just odd it only works without the motor shield, but I'll do some more research, and trouble shoot a bit more.
It sounds like the motor control board is shorting out something on the Arduino. There should be no other way for the motor control board to prevent the power light from coming on when you plug in the USB cable. 
On one lucky occasion I have seen the motor shield and arduino lights turn on for just an instant, then turn off when the motor shield was fully plugged in.
randomnoob2:
On one lucky occasion I have seen the motor shield and arduino lights turn on for just an instant, then turn off when the motor shield was fully plugged in.
Still sounds like a short. If you can upload to the Arduino with the shield detached there must be something wrong in the shield hardware.