The bent shackle bolt is no big deal, either replace it or straighten it out. Its a soft grade bolt. The shackle pins have a taper end tend to hold them self in place, but a small clamp wouldn't hurt for a safety if you plan on removing the bolt. You should jack up the frame a bit to relieve the spring pressure for safety as well. On my '37, the shackle pins are threaded in to the spring bushings, so if you try to remove yours for cleaning or inspection, try to unscrew them.
Center bolts can be bought at any trailer supply house or spring shop, I have used allen heads before with no trouble. The center bolt is only there for alignment of the leafs. Its a soft bolt and serves no real strength to the suspension. It does locate the spring to the axle so it needs a round stud like head (allen head). Using c-clamps is a good way to replace them, the leafs are not going to fly across the yard if you let them loose. The spring clamps out towards the ends of the pack will hold most of the leafs in place. If you wish to undo the hole pack for cleaning and inspection, you will need to bend the clamp ears back to work the leafs out. These clamps can also be replaced with hardware store bought steel flat stock and a heavy duty rivet or counter sunk screw. Replace the u-bolts if removing the leaf springs, they are a stretch type bolt and will keep stretching if you keep tightening them, new ones are cheap and good insurance. These are what hold everything together.
Joe