Thanks for the suggestions I did manage to get the ships unstuck through opening up the .sfs and vertically moving each ship up a little.
If you wanted to know what the problem was I put some images up on imgur.
So after a while of playing and finally making it to the Mun I landed saved the game and quit for the night. But coming back my ship was halfway stuck into the Mun and when I try to take off it explodes once the engines reach the surface. Cant seem to find a fix for this anywhere online so I may as well ask here.