from what I see, it looks like those are grub screws that you would use to help secure the pivot balls to the upper and lower arms. see if those little metallic spacers fit into the holes before you put the grub screws in. if they do fit then most likely they are there to prevent stripping of the screws themselves when over tightened. That would be my best guess based on the pics you provided.
as far as your shock problem goes, i guess it is possible that integey mass produces so much crap, that they overlooked a true fit for even their own products. it doesn't look like the shock caps fit onto the pins right that you use to mount them to the towers.
the other parts you have left over look like plastic body mounts for the front and rear. the round shaped alum. spacers look like the same pieces you'd use to mount the posts to the shock towers.
reassemble, haha then burn it. I'm not a big fan of Integy. and yes one would think that instructions would come with their products since they make aftermarket parts for every single part you can find for the T-Maxx. yes, I do have a few integy parts, but they are simple, non moving, and not crucial to performance. (i.e a wheelie bar)
I swear they just build parts for the masses without actually testing out their own products.... just cause they look cool... cause if they did, then I'd like to know how the hell they managed to tune a 2.5 engine with that quad exhaust kit they make.... its just not possible... unless their defination of "tune" is to keep it neatly stored sitting on a shelf in your basement. (see also, paperweight)
post some more pics of different angles, a few close ups and a few further away. its hard to see the relation to it when its only closeups.
also, post a few more pics of different angles for the extra parts themselves. I'm pretty good at figuring these kind of things out visually, but i need to see the big picture.
it alsmost looks like the post mounts themselves act as the spacer you need for the shocks. if they mount low enough on the chassis that may be the issue.
if this doesn't help, try to google a pic or 2 of fully completed integy kits and see what comes up. seeing the finished product could shed some new light.