When upgrading the big three i cut the Battery negative to chassis wire and just hooked up my own to the frame is this a problem or should of i left the stock one? Everything runs the same as before

 

A wire is a wire. As long as your connections are secure you won't have any problems.

 

k cause the tutorial i was using said to leave it on but i forgot and clipped her

 

There is no harm in leaving the stock ones, but there is also nothing special about them that means you need to keep them. If you are sure that the two items that were connected are still connected then you're all good.

 

there is no harm done
your cars cpu may need to reset and it will after you go for a drive (if your cpu in a car that you undo the neg or pos thay reset after thay have power and once you drive it )

 

Is there a problem wiring the positive battery post straight to the alternator positive, we are having trouble locating the stock one cause the wires change color and all sorts of things? If there is no fuse will i fry the battery?

 

no, your car will just burn down. fuse the line, its a good idea.
if your car is a daily driver and not an spl car and thats it, better fuse.