Thank you, I appreciate your comment and support, as it has spurred me to give it another go, and now I'm happy to say that I have managed to remove the top colored part of the 3DS XL case. There is some confusion and collateral damage as a result, but I think I more or less got it down.
I figured it out off a hunch from the DSi XL. In my experience the two systems are built very similar, so I figured I'd look up the teardown for it on iFixit and try what they did there.
First step was to remove the four rubber pads on the inside of the top half with a scalpel or similar tool. The screws underneath are Phillips 00, like on the rest of the system, so use one of those to remove them and set them aside.
After that is the part that kept me guessing for a while. What you have to do is find the edge between the top cover (the colored half) and the bottom cover (the black half) of the top of the case, and, using a wedge, carefully pry the two halves apart. There are numerous points all along the edge where the two halves are connected, so you have to go all the way around, including the hinge itself. If you close the XL, you'll see that the edge between the two halves of the top of the case extends through the length of the hinge as well. Thus you will have to do the same prying apart there to fully remove the top half.
Once you've done all that, you can just pull the top half away and be greeted by the inside of the top half of the system, including the screen, speakers, cameras, and 3D depth slider. If you only want to paint the top part (like I do) then you can set this half aside. I haven't done a teardown of this yet, but if I end up busting this 3DS XL then I'll go ahead and do so (after a new system and a transfer at least!)
At this point you're just holding the colored half of the top of the case. Flip it over to look at the inside, and you'll see along the top edge the holes for the camera lenses and the 'camera in use' LED. The two lenses each have a black border around them, this is in fact made from two pieces of plastic which are taped in place. You can simply lift up gently on the tape and you'll remove them, and they should go back in pretty easily when you're ready to rebuild. Next you can take out the LED plastic bit by simply grabbing it with some tweezers and pulling it out. It is held inside of some rubber padding, just pull the whole hting out (padding and LED part) and set it aside, it will also fit back in quite nicely.
Thus are you left with just the top half and no other parts, and it's all ready to be prepped and painted. Hope this writeup helps someone.
Now, there are a few issues with how I did it. The first biggie is that after opening the top half, I found several small bits of plastic fell out, which means I screwed up. My tool of choice for opening them was an old novelty flattened penny, but I'm sure that there are much better tools to use which will open the case without damaging the case. These I believe were once the plastic clips holding the system together, however I hope that with how many plastic clips there are and how firm the whole system was to being opened that the loss of a few will not be a big deal. Regardless I don't recommend testing your luck with this.
The second issue is that some odd bits fell out which I cannot identify. They are two rectangles, one made of what seems to be shiny thin black plastic and has a rectangular hole cut out of the middle of it, and the other which is a whole rectangle and appears to be made of a very fine mesh material. I do not know what these bits are or where they go as they fell out of the case as I was opening it. I cannot give any rhyme or reason as to where they came from or how to open it without losing them, I can only advise that you exercise caution when opening it up so that you don't end up where I was.
Now finally, I think I might like to make a new thread for this and post some pictures. Hopefully I can attract some attention so that others who want to do this can do so, and better yet that more experienced modders can take a crack at repeating my exploit and hopefully do much better job of explaining it and documenting everything.
Note, the picture I uploaded still has the lens and LED bits in it, they're really easy to remove though as I said.