Just cleared the last planet last night. The last two production stages stymied me months ago and I got frustrated by the fixed reactors so I put the game down. But it's been nagging at me periodically since then. A couple of days ago, I took another look at Σ-Ethylene and the solution just jumped out at me. It was all of a sudden so obvious. It's hard to imagine what stopped me up before. Even just my brute-force solution came out way below the 6000 cycles needed for the achievement.
Bolstered by that, I turned my efforts to Ω-Pseudoethyne. Now, that one is proper fiendish. I couldn't for the life of me work out a solution that incorporated the loopback in the second reactor. So I just built out a bigass sorting reactor to break down the Ω-C chains and alternated in whole H2s in parallel. The second reactor sorts the fragments and bonds the final molecules. It's not clever, but at least it's fairly tidy. The only trick is being careful with the order you output the first reactor so the inputs on the second reactor are sort of predictable.
Flip-flops are easily the most interesting control element. When going back to look at old solutions, I'll see a beautiful solution but then I'll remember that I don't have flip-flops yet and I get a little sad.
If you're just chaining flip-flops one to the next the number of cycles they'll give you before they dump out is just N^2. With just that, you're limited to powers of two (2, 4, 8, 16, etc). You can get tricky with it by running parallel chains or by priming a flip flop running a waldo past it without actually hitting its loop or running a bypass inside the first flip-flop loop so you run a dummy cycle through it first gate.
My fast-ish Σ-Ethylene solution uses a six-loop flip-flop matrix for building the C2. It looks something like (f>F)>F, if you understand the notation. The first two flip-flops grouped should give me four but the first one is pre-flipped by a dummy pass, so it drops that cycle, leaving three. Then that group dumps into another flip-flop so that doubles the three to six.
Man, SpaceChem. So good.