The first thing that you need is a Honda Rebel 500 Service Manual.
What you need to do to the bike is not that complicated but it will be awfully hard for most of us to verbalize the instructions.
After acquiring the Service Manual you can go to Ron Ayers, or one of the parts places, to find out the pitch and length of the fasteners that you will need.
After knowing what you need for fasteners I would go to a good nut & bolt wholesaler in your area to acquire the bolts.
Honda uses lousy fasteners and some of us have replace many of the OEM fasteners with aftermarket fasteners.
! - I've got a pdf of the service manual and I've spent most of the day going through it. Unfortunately, it's very detailed in the parts that I already have down, but lacks detail in the parts that I'm missing :/ - it's not helping as much as I would've hoped. Fortunately, with a trip to the hardware store I was able to identify two of the bolt sizes and grabbed them from an ACE in town.
Unfortunately though that still leaves quite a bit of unknown on this bike. I get it on verbalizing the instructions - I wonder if someone could take a few of pictures (color - as compared to the service manuals greyscale) of how things are supposed to be connected.
In particular, I think i've narrowed down my needs a bit.
1) The plastic "bin" that holds the battery / fusebox. Mine is connected towards the front of the bike, but the rear is just floating freely - not connected to anything. How should this be secured to the bike? Additionally - the sides of mine are completely open with two empty holes that according to the service manual - there are bolts that should be in there - but again nothing to fasten it to. Pictures 11 & 12.
2) The metal piece to which the rear of the seat fastens. On my bike that is also free-floating (save for the wiring harness that goes to the heat-sink underneath it). The bottom of this piece is pictured in No. 6. According to the service manual - two bolts fasten this - but again my bike has nothign to which to fasten it.
3) The battery cover. This too is currently free-floating - not attached to anything. I see two holes where it should be fastened - and it appears in the service manual that it uses fastening clips instead of screws - but my bike has no holes to attach it to.
The common theme is things are free-floating; i'm hoping theres only one or two pieces that i'm missing - and that is what ties the rest of the bike together; i'm guessing this was thrown out in the removal of the rear fender.