i just finished a ls swap on a civic but everytime i run it and shift just a little hard it sounds like something is grinding and then about ten seconds after it sounds like something fell out of the engine bay i thought it was my cruise cotrol bouncing around but its not i know its not much info but i cant seem to figure it out

 

What kinda shape is the tranny in? Grinding while shifting is usually syncros. You can open the tranny and inspect if you feel good with tranny work. As far as something falling out..... Have you checked and rechecked all the bolts that hold EVERYTHING together. (since you just did the swap) Are all your engine mounts and brackets in good shape?