You may have also bent the deck when the spindle housing got tweeked. The last carriage bolt nut can be accessed from the underside of the deck. If the deck it bent up, some heavy washers, a nut and bolt and an impact wrench can be used to true it back up.
For the spindle bolt, you "might" be able to smack it with a really small cold chisel and get enough bite to turn it out with the chisel. Otherwise Kevin is correct.
You will need to drill a pilot hole in the bolt and use an "easy out" (there's an oxymoronic name eh?) to get it out. Start with a larger, stiff drill bit to try and create a centering depression in the bolt and then go back with the small bits and work up to the size you need for the easy out. If you start with the small stuff you will end up walking the bit to the edge of the bolt and gumming up the threads....
Not that I have any experience with either of these issues...;-)