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The output molecule is an alternating series of layers, so you have to build it up from the top, joining a new layer each time. So what you do is build a layer on the left, move it to the top of the output area, bond, and then move on.
Since the bonds between layers alternate, also clear is that the output molecule needs to move one tile left or right with each new layer.
For the building area, keep in mind that you don't necessarily have to move the Carbon atom at all. If you place a bonder underneath where it will appear, all you need to do is move around the H-delta-H molecule, stripping off one H, bonding, and then bonding the remaining H-delta to make a straight H-C-delta-H molecule. Which then needs to be either rotated or bonded to the main output molecule as is.
Once the program gets to the third cycle, the subunit is misaligned and there's no room for additional instructions to put it in the proper place. The only way to fit more instructions in there is with flip-flops, but because flip-flops take an additional space on the bottom row, I can't move the subunit across a flip-flop without putting it out of bounds. I've tried moving the whole assembly one place to the left but then it starts to collide with the rotating subunit. I might be able to remedy that but it's gonna be an ugly fix.
The next level was child's play in comparison. Ω-pseudoethyne and ∑-ethylene, however, leave me immediately stupefied. It doesn't help that the same problem is staring me at the face in 63 Corvi. Maybe I'll go back and try Moustachium 608.