Both are good solutions. See this thread
for how I usually mount them - just some screws.
I can't really say which would be better other than that the floods might be a little harder to integrate since the rest of the build is not set up for them. Construction of the original bars shouldn't use Arduino or the crazy circuit anymore, just a BuckPuck and some Crees.
A few other notes. Regarding your card-unloading question, some people have used Eye-Fi cards to do that over wireless, I haven't, so I can't help there.
Regarding the build as a whole, it has a large number of unnecessary screws because it was a prototype. Consider cutting a single part, like one of the arms, and gluing it instead of screwing it. It should result in a more sturdy part and cheaper/simpler construction.
Also burn a few test parts to check fit.
Would you consider changing the title of this thread to reflect the scanner you've chosen to build?