Looks like random hardtop brackets and screws. The two big ones go up top in the roll bar. I think the the other brackets go in the rear, between the lip of the hard top and the side of the Jeep. it is how the hardtop is screwed into the the Jeep....I think.
The two knobs are for attaching the hardtop to the body @ the sound bar, the torx bolts and the metal clip @ top right are hardware that do the same but @ the
bottom of the hard top. (there is a track/depression on the body. Look under the flat surface at the top of the rear of your jeep where the hard top sits, you will see there should be 3 on each side) not sure about the rest of the stuff. Mine had 2 extra clips and 1 extra torx machine screw. Random!
My 2011 had a hardtop as does my 2012 and those two big knobs are nothing like the knobs used to fasten the back of the Freedom Top panels to the sound bar. And the main hardtop is fastened with four screws on each side. One each at the B pillar and three along the rear side.
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Those knobs are smaller than the ones for the hard top, and are made out of hard rubber, correct? These knobs, with the brackets installed go through the loops where the hard top clamps clamp onto, and screw up into the front rail of the Trektop soft top to pull it down and secure it. I think the washers, shown there, are also small enough (can't tell by the picture) to be used with the knob. My Trektop (Not Trektop NX) uses these exact pieces.
After a nights (or days) rest, I concure with 2008jk - the green circle is the wrong shape for the rollbar screws as well, I didn't even notice that until today - so much for doing things when I tired.
Green - These two are for the holes in the roll bar. Don't over tighten them, they will never stop spinning so just get them snug.
Blue - this slides behind the rail on the rear of the tub where the last hardtop bolt is. It will slide into the edge of the tub and the bolt will go thru the hole.
I have a Bestop Header Safari Bikini top that uses the yellow and green parts. The yellow is a plate that fits over the metal loops under your visor. The Green parts are knobs that fit thru the (yellow) plate and through the metal loop and screw into a bracket bar that holds the sun shade top in place. So...yellow and green parts work in unison.