RE the spikes: I originally had a different layout where the first spike (and the coin) was supposed to be a puzzle element you had to be careful with... it didn't really work. At all.
Like I said before, the design process for the layout (not the plan, which I knew from the start, just the layout) involved some trial-and-error, so by the time I noticed the spikes were actually completely pointless and I could've just not had them... well, whoops, I already got attached to the whole "spooky means spiky" idea and kinda just left them for the mood. In retrospect, simply walling that part off and not having these spikes/coins at all would probably be
more visually elegant, but making a version B just for that alone felt really pointless.
As it stands, the only way you can mess up the spikes bit (other than, you know, accidental impalement) is by collecting these coins too early -- the top coin is actually a necessary blocker. Aside from that, there's no real puzzle to the spikey bit at all, so once you do everything else, you're free to collect these coins. Just be a bit careful to make sure Stinky's feet are alright.
There's some ingenious thing I'm totally missing, and I've no idea what kind of thing it is.
Well, you do have a few good leads. You're right that the green timer needs a box... and, while your
specific idea of where to use the link spheres is wrong, you're absolutely right to recognize their importance. These overworked blue heroes do A LOT in this stage, a lot more than just pressing buttons...
and even if I somehow do that, I still can never free the link sphere I put down there, resulting in being unable to push both the purple and yellow buttons.
... and deserve a bit more gratitude than just getting shoved way to the bottom and being stuck there.
There's one other very important thing they can do for you without becoming irretrievable. If you can figure that out, you might also figure out what central lie is working overtime to steer you away from the solution. Misdirection is, after all, the art of lying with your layout by planting false suggestions, and the false suggestion I'm planting here is... pretty brazen.
Once you figure out where's the lie, the rest should become a lot easier. It might help if you try to imagine yourself breaking the level as much as possible, the way I did to a few official levels -- what's the absolute oddest thing you can try to do? What are the
least likely things that you can try to pull off? One of those ideas might just be THE trick...