With all my parts all over the place Im tring to figure out what the bolts that run from one side of the frame to the other that are located right above and below the area where the swingarm and frame come together do. They are the allen head bolts. I thought they ran through the motor like a brace but now after looking Im not sure....

lol, yep allen head bolts, 1" 1 1/2" long.

Bolt to the Y shaped brackets that do have bolts that go thru the engine.  

Next time get like a muffin pan and then you can use tape or something and label where they came from. Can be pretty useful!

Lots of ways to help keep up with where bolts go. Sometimes a bolt can be put in the hole, with the part laid to the side that WAS held by the bolt. Or, tape the bolt to the bracket that was removed. A piece of cardboard with the area being worked on sketched on it & slots poked in the proper places , that will hold the bolts. This is very handy on the sidecovers.