If you look at the pic of the complete bike, it will give you an idea on placement. It's really a personal preference. If possible, clamp the rearsets close to where you think that you want to mount them and then sit on the bike and see if it is comfortable for you.
Most of the newer rearsets come with the MC mounted and attached, but sometimes the angle doesn't work when retro-fitted to another bike. You might have to end up welding some additional tabs to the frame to mount the MC.
You will likely have to shorten the motor mount bolt after you remove the stock footpeg brackets. If you can shorten it and rethread the end, then that's the best option. If not, cut it off and weld a slightly larger nut to one end to make a "bolt" out of what was once a double ended threaded rod.
In all likelihood, the shift rod won't be the correct length. It will have to be lengthened or shortened. I usually cut it in the middle, place it into a piece of aluminum angle to hold it straight (the aluminum won't stick to the steel weld) and weld it back together or weld a longer piece into the middle. You also need to look and see if the piece that fits onto the shift shaft will work with the Honda parts. There are a couple of sizes of shift shafts used on bikes and some have finer or coarser threads. If need be, you might be able to cut off the stock shifter and add a heim joint to it.
The new shaft shaft piece on newer stuff is likely aluminum and therefore can't be welded onto the stock steel shifter. Also, most shift linkages are set up with one right hand threaded heim joint and one left hand thread to make final adjustment of the shifter height easier.
Also you have to tack the mounts to the frame and make sure that the pegs fit perpendicular to the frame. If the bracket is not exactly straight, then the peg will angle forward or backwards. Again, tack it into place on both sides of the bracket before final welding.
TR