@bass32 Yes for your first point the fretted the E string on the 5th fret and that is A and once i played open A it did not match at all so once i got the 5th fret of the E to match the open A string the open note of the E string was an F and i will probably end up taking it in to get set up
I really think, it's just an issue with how you're tuning the bass, and my apologies if I'm wrong and keep pushing the issue, but if you tuned your bass like how you said above, then you would definitely have issues. You should have tuned the open A string to match the 5th fret of the E string.
When you tune the E string, using a tuner, and fret the 5th fret, then you should be playing an A (unless your intonation is off, which is possible, in that case tune the bass using the method I posted in post #6). Your A on the 5th fret of the E string should be what you use to tell if the A string is in tune. Since you already tuned the E string, you know that is tuned properly and so should the 5th fret. So if the open A string does not match, then you must tune the A string to match the E string, not the other way around, as what it sounds like you are doing from your post.
You're E string may be bottoming out on the first fret to get an F, but then I don't know how you would have ever tuned it to an E in the first place, and playing the 5th fret would still give you an A.
Again, I apologize if I'm wrong. I'm just trying to help you out, and from what you've written, this is the impression that I've gotten. I don't mean to sound like a d***.
EDIT TO ADD: You posted this is post #3 "first off i started an tuned the e string and then tuned the rest of the strings accordingly and once i started to check to make sure it was intune the octaves did not match up at all and then i tuned the 5th fret of the e to match the a string and it ended up being an F".
The thing is is that if you tuned the open strings to E, A, D, G, and then the octaves were off, that's what you should focus on first because the 5th frets ARE going to be out of tune. I would really just start over, and tune it to how I mentioned in post 6 and not worry about the 5th fret, because it would take care of itself in that method.