What is the best way to merge subfigures and convert to a required format for submission to a journal? I'm currently preparing a paper for publication and so trying to construct the figures. I'm finding it more difficult than making figures for a report mainly because journals expect one figure file for each figure, regardless of whether it contains subfigures or not. This leads to some problems/hurdles:


I can't use LaTeX's \subfig package, so I have to manually place an (a), (b) and (c) on the figure and keep track of the caption if the ordering of these changes.
Journals' rules about figure submission vary quite a lot, some can take pdfs, some want vector graphics, others raster.
I have to somehow merge the output from various programs into a single file; for example diagrams made with Tikz make up the same figure as a graph plotted with python's matplotlib.
With having to merge subfigures in such a way, my workflow becomes quite convoluted if I have to modify one of the subfigures, and then regenerate the single figure file.
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.