What is the best way to merge subfigures and convert to a required format for submission to a journal?
I don't know how well this will apply to you because I don't use tikz much. But if you can save them as say a pdf, this might work for you. 

I use illustrator (but inkscape is similar and free), and I link in the files so that if there is an update to any component it will update. And I merge them all together. 

Then I can just save it as a pdf or svg (or whatever format the journal wants). I found this a little cumbersome to start off with, but now that I'm used to it, I have a hard time reverting.