I can't speak to the software side of things, but good processes and planning are the ticket for shop efficiency. I set up cabinet vision to give me a lot of the needed things with reports and labels. The last shop I set up as paperless with a few ipads, Each job is split by room, for each room there is floor plan, elevations, build sheets, door lists, drawer lists, etc. Each job is color coded (red, blue, green, etc) and each room has a different starting cabinet #, so for example the kitchen starts with 100, the pantry starts at 200, etc. Part of the engineering process is to add toe skin, crown, riser, scribe, etc as individual parts within each room, now these parts have an assigned cabinet # so it can be tracked. By having color coded labels on parts it speeds up finding the parts you need as you only need to look at the blue labels and can ignore the red & green ones.
There's finished project reports that list all the cabinet numbers and names so it can be checked prior to shipping and/or at delivery. And since all your trim parts have a cabinet number (and build sheet) you're not going to miss things as easily.
I typically renumber the trim parts so they are all at the end of the build sheets so they stay grouped together, like cabinets 100-131, but then the toe skins are 199,198,197,196 etc.
One of the best things is a paperless shop, no more losing pages, losing notes, etc. the "oh I forgot the scribe, or I didn't make enough" is harder when there is a build sheet/cabinet # assigned to each piece.