There is no trivial way to do this with Automator.
Automator does have the ability to create Folder Actions which automatically run against files dropped in a folder.
Additionally, it does have the ability to rename those files, naming them sequentially, but it's not smart about how to do this - most notably, the 'Rename Finder Items' action will rename those files, but not take account of existing files when adding the number sequence.
For example, assuming you drop three files into the folder, and they get renamed to 'file-1', 'file-2' and 'file-3'.
You then drop another file into the folder, expecting it to be renamed 'file-4', but the Automator Action will NOT do this - it simply considers it as 'file-1' since it is completely unaware of the existing file number sequence in place.
In other words, it's a once-and-done approach that cannot be used repeatedly. It's OK if you want to drop all 7500 files in at once, but that doesn't sound like what you're asking.
However, you cannot embed a Folder Action like this inside a larger workflow - Folder Actions are specifically built to react to changes to folders on disk. You could have one workflow creating your screenshots, and a separate Folder Action workflow that renames the files as they're added to the folder, but the issues above still apply.
Additionally, the problem is compounded by the very first statement in your post:
> I am currently running a pretty lengthy and looping workflow in automator
There's no way to sugar coat this. Looping in Automator *****. It is orders of magnitude worse than any other scripting or coding language I've ever used, to the point where I usually look for any other solution if a task includes looping.
To that end, I recommend refactoring your workflow.
I would consider splitting the workflow into separate tasks - for example, the main workflow does all the work to create your screenshots, then you kick off a second workflow (not a Folder Action) to rename the files once they all exist.
Or you refactor the renaming script to have additional logic that maintains some kind of counter, or is aware of the last-used sequence number and renames the files more intelligently - this cannot be done by Automator directly, but could be achieved by an AppleScript embedded within the workflow.
The one thing that Automator does do well in this case is avoid the issue of the newly-renamed files triggering the Folder Action again - conceptually, when you rename a dropped file, the renamed file appears as a new file in the folder, and triggers the script again. Automator handles this, but other models may not. For this reason I recommend a staging folder - have the main script save the screenshots in a temp/holding folder, and have a folder action (or other script) process that folder, moving the files to another folder as they are renamed.
At the end of the day, it sounds like your workflow is complex, and you will benefit from breaking it into separate modules rather than trying to craft a single monolithic entity to do it all.
