Hi Nathan- 
Attached are electronic versions of the spectra from z543. 
v3e.ufo is the spectrum in relative units, corrected for instrument response. 
The absorption lines appear superimposed on a sereis of bumps and wiggles that I dont believe are real. 
To find the approximate transmission I first edit out the spectrum line by hand, then filter the spectrum. 
This edited/filtered file is v3blin.ufo. 
Then to get transmission I divide v3e by v3blin. 
The approximate transmission is file v3elin.ufo. This is the "line transmission" that we have defined in some of our papers. 

Z541 and 543 were very similar, but not identical. 
I analyzed z543 because it had the best signal to noise. 
The power/energy was higher on 541. 

I have a memo from one of my Colleagues (Mike Cuneo) that has 
                             z541               z543 
Energy (MJ) 1.7 +/- 0.1     1.45 +/- 0.1 
Power  (TW) 166                  134 

I'll be gone for a couple of weeks, I'll be interested to see what you come up with. 
This experiment was never really exploited for physics results, could be some interesting insights available. 

Jim