So I've tried dividing every connection or value I could find and removing/re-adding the existing factory I had wasn't updating. So as a quick-ditch effort I crafted a new factory and BAM, the outside connections lined up with the newly sized factories. The issue I have now is the inside of the factory being completely out of whack (likely from my last hail mary which divided way too many values in half when in reality I believe it was a small handful that were needed [will update this post with the exact values just in case someone else wants to know]). Makes sense that the existing entities would retain previous values if you need to move a factory.
So everything that needed changing was in the layout.lua (by everything, this does not include the original resize of the factory entities, which need are in prototypes/factory.lua and graphics/factory > resize images and match them with the factory.lua file. The layout.lua changes that were needed to be made were:
outside_size, outside_door_y, and the first two values of the connections arrays all adjust the outdoor layout
I'm still unsure of the overlay section. I've gotten the belts lined up semi-close but realized a few issues from reducing collision and selection boxes to half their original sizes shaved off .2 of their original values, and for some reason shifted to the left about 0.75, so an offset had to be introduced to the collision/selection boxes which I'm still working on centering, after which the belts need to be shifted to match. Thanks for your help in this, only has taken about 10 hours or so (a lot more work than I originally thought but didn't think about functionality on my first biggish modification to an existing mod :P )