It looks like you found your problem, although a little odd that you lost all of your bolts. If the engine wasn't spinning the pump then you had no pressure. You need to get bolts that are the same grade and length to replace your missing ones. You'll probably have to rotate the flywheel a bunch of times to get the holes in the right place as I think it will only bolt together in one position.
Be sure to use thread lock on each bolt and you should be back in business. Be sure to check your tranny fluid level as soon as you get it going. Good luck! I had two bolts come out in a car once and it sounded very loud and much like engine damage as they were rattling around the bellhousing.