Weep for I have wept.

First of all, great puzzle. Or in the words of spiritualshampoo "cringe"

Took me 4 days of banging my head against the wall to find a layout where all atoms could access the glyph of duplication until I realized the second input can help. 

Then I attempted a solution which intended to have 3 fire grabs but which unfortunately worked up to 5 (sucks) and has a super extensive end just to fix ONE triplex bond I forgot somewhere. I'm pretty sure I've figured out all the techniques to get 0 but I don't have any energy anymore.

Programming this took 3 hours. Programming min cost is actual manual labor >:C

Only redeeming part of the solution is the fun loop input 2 makes at one point while input gets blocked. I enjoyed that part.