@Jasondm007 There are a few things going on here. Firstly, the Replace util should work fine when passing in a JSON configuration (Just tested this, not a bug), but in your workflow, you are passing matchmode as 1 (REGEX) instead of 0 (String), so things won't be processed as you expect.
Secondly, @deanishe is correct that there is no actual input query being passed in to process the find and replace on, so you are essentially asking Alfred to do a find and replace of no string at all. If you want to act on whatever is in the clipboard, you could add {clipboard} as the argument in the Arg / Var utility before the Find and Replace.
It's also worth noting that when it comes to the find / replace, you don't actually need to configure it with JSON, you can configure it inline like this:
Here is your workflow (simplified) which does the find and replace based on your given arguments for the current contents of the clipboard:
https://www.dropbox.com/s/mxxkiggrqa8gy1o/Text - Find %26 Replace.alfredworkflow?dl=0
To access the context menu, you need to bring it up and simulate the click. The alternative is to perform the task itself some other way. It used to be possible by using the Dropbox API, but it’s unclear if it’s possible still without major hassle (creating a new Dropbox app, setting up OAuth…).
If you do find a way to make it work programatically, we can help you integrate that into Alfred.