Is there some sort of software or app. that you use for keeping sorted your transcriptions, digital imaging, and other things like translations and standardised punctuation?
Other manuscript work discussion is welcome, but I'm mainly trying to work around the limitations I'm experiencing with Microsoft Word.
I'd also like to also find an editing programme for creating interlinear notation and translation.
There is not, as far as I am aware, any such software.
The standard practice, at least around me, is to copy a transcription out on paper and then type it up. This two-stage process catches many errors.
What problems precisely are you having with Word?
There are programs like Scrivener that are designed for preparing papers and books - they have basically nothing in terms of layout tools, but are instead more like databases that bind together versions of texts with research and images and anything you can throw at them.
I use Scrivener for writing and research.
Since you're familiar with Office you might also try OneNote, I used it to take notes in college and I was surprised at how flexible it is.