Jerod is exactly right, do one side at a time. Loosen everything on both sides (don't forget the two in the very front) and then jack up one side an inch or so. You can then push the bolts up and slide the bushings out.
I don't know where you can get new OEM hardware, maybe from the dealer? LC Engineering sells urethane bushing kits for the gen1 4Runners and I bought my new OEM height bushings from them. I would recommend them and they aren't that expensive. I think it's about $100 for new bushings for the entire 4Runner which includes body bushings, torque rod, sway bars, etc. or you can just buy the body bushings for quite a bit less. I don't think they sell the hardware but you could check with them. Here's a link to the body bushings ($61.95). The page with the entire master kits is a few pages earlier.
Part Listing - LC Engineering, Inc. (GUEST-Contact) -
In theory, you could buy the body bushing kit and then remove the old bushings and hardware and modify the hardware to work. The kit comes with the washers and metal inserts (metal bushings that go inside the urethane bushings) so I think you would only have to cut the bolts to length.
The "nuts", which are large and flat (some with retaining wings) sit recessed in the 4Runner body. I would install one of the new bushings with the old bolt and see how much needs to be trimmed off. It might not be as much as you think and you can get away with a bit of extra length because they are recessed into the body anyway.