Where are you located? It sounds like you may be in a little over your head. Replacing just some internal pieces on an f3 is a much bigger pain then just replacing all the internals at once.
The manual doesnt explain how to do this stuff simply because Jotul doesnt want you repairing their stoves, they want their techs to do it or sell you a new stove.
But here goes, I fully rebuild and restore more F3s than anybody else so Ill try to help.
The reason nothing came out easy is because something is warped. Normally its the rear burn plate and the right burn plate, everything should pop in and out easily. Its normally people burning with the ash door open that ruins all the internals.
Once you have the new grate in, then put the new insulation for behind the back plates/side plates. Then install the rear plate and both side plates. Now you need to set in the baffle. Before you put the rear and sides in you should have replaced the 3/8”ld gasket on the back wall, its what the baffle sits against to keep the air coming in, going into the baffle. If you have never replaced the baffle itself before, then its most likely due to be replaced, or rebuilt, its just cement keeping it air tight.
Once you set the baffle in get it to line up with the screw holes in the back, but dont knock that new gasket on the back loose. Now you should just get new hardware, anything from the hardware store works. They need to be M6x1 and the same length as what was on before ( slightly longer ones for the through the back to attach that baffle sometimes makes it a little easier) now insert the bolts from the back through the back bottom of the baffle, remembering the one side has the air cover on it as well. Its also good to note here if your f3 doesnt have an air blocker under the rear air cover, order one and add it in there. Now tighten those down a little.
The next bolts are the front ones on the top that attach through the side plates and the baffle vertically, you will need to play around to get it to line up if you didnt replace side burn plates as well. You will notice the screw heads on the underside of the baffle coincide with 3 spaces on the burn plates, you want them to line up so when you tighten the front top bolts, it will be as flush as possible between the baffle and side plates. You can also put some of jotuls flat gasket on top of the side plates where they meet, ive seen it done both ways.
Once everything is lines up, I tighten the back first 80 percent hand tighten, then the same with the front ones, then finish them all hand tight or a little past.
Now since you are here already, Id take the 2 10mm bolts off the front inside top that hold the airwash in and replace that 3/16ld gasket as well, it will help keep the glass cleaner.
Now you just have to replace the gasket on the top lid with 3/8ld, place it back on the stove and center it, and use the set screws on the sides of the stove to tighten the top down, verifying with a flashlight looking up and in, that the set pins did indeed make it through the holes on the tabs.
And thats pretty much it!
And to answer your other question on where to find most of those gaskets and parts, you can reach out privately to me. I sell most of it through my private wood stove restoration shop.