In this context I would like to ask you few things:
1. (I may be wrong) I saw that post-minify, the script files appear in the footer (which is what it should be). Meaning along with minification it also places the javascript, jquery files at proper locations. Is it true?
2. If I just pick the script files, and minify externally, replace the content back to original files. Will it work or break my site? (say, I disable the minify plugin).
3. Could you explain this "estore plugin is broken in that includes javascript files that don't exist"
4. Do the scripts of wp-cycle and eStore plugin are similar and hence clash?