ok, so it works if I ok errors on every bibitem lol.

With the prior comments pdflatex and lualatex appear to work
on my document until I run bibtex. If I modify my build script,

LTGT=lualatex
# wtf? needs to click through errors now? lol
# XL="$LTGT -file-line-error -halt-on-error --recorder "
XL="$LTGT -file-line-error -interaction batchmode --recorder "

it looks like it works on a quick inspection but there
are obvious problems. The reason I tried that is from
the command line by hand, running pdflatex with a bbl
file produces this kind of error, see output below.
Looking more closely however the bibliography
becomes the last part of the pdf file dropping
the following appendicies that exist when there is no
bbl file entry. 
Is this another well known simple thing? Thanks. 


Overfull \hbox (10.0pt too wide) in paragraph at lines 129--134
[]$[]$ 
(./copper.bundle_checksums [50])) (./copper.bbl
! Missing $ inserted.
<inserted text> 
                $
l.3 \bibitem{Abdolmohammadi_
                            Sharma_Copper_Deficiency_Forgotten_2011}
? 
! Extra }, or forgotten $.
l.3 ...di_Sharma_Copper_Deficiency_Forgotten_2011}
                                                  
? 

LaTeX Font Warning: Command \em invalid in math mode on input line 6.


! LaTeX Error: Command \itshape invalid in math mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.6 \newblock {\em
                   Blood}, 118, 11 2011.
? 


-- 

mike marchywka
44 Crosscreek Trail
Jasper GA 30143
USA, Earth [email protected]
 404-788-1216 ORCID: 0000-0001-9237-455X