Could you be more specific about the awkwardness of the controls? And what do you think that made the instructions (and everything else) confusing?
I think the alchemy controls are awkward because of the number of keys involved (arrows, A, S, and Space) and because the interface switches between two 'modes' (adding pieces and removing pieces).
Also, if you count the recipe page (which I had to look at a lot until I figured out how the recipes worked) then that's another two keys (Enter and Escape, as well as having to scroll to get to the right menu) and an additional 'mode'. (Showing the recipe next to the apparatus would get around that.)
Doing something that feels like it should be quite simple, such as moving some assembled pipework one row lower in the grid, takes an awful lot of key presses.
If the game was controlled with the mouse (and I can understand that you'd want to stick with the keyboard for everything) then the controls would be obvious: Click on a piece, drag it to where you want it, let go (and if you're dropping it on top of another piece, then the old piece flies back to the table, or something). Could the keyboard controls be similar to that? Move a 'hand' cursor with the arrows; press fire to pick up a piece; press fire again to drop it (or switch it with the piece below)?
I found the first puzzle in particular confusing because of the amount of new stuff I was being confronted with. As well as getting used to the controls, the player needs to interpret the recipe (there are two lines to it, so presumably the recipe has two stages... doesn't it?), work out how the apparatus are supposed to be used, and solve the actual puzzle of following the recipe using the limited range of available pipes. And there's no feedback that you're doing it right until the puzzle is solved.
A couple of suggestions for things that might make the first puzzle a bit less overwhelming. First, let the player see a completed alchemy puzzle earlier in the game (just as an interactive bit of scenery). Second, provide more bits of pipe so that there are more ways the puzzle can be solved.
Just my opinions of course. Overall I think the alchemy puzzles are really rather good, niggles aside.
Simon