Hey, there is great software for scanning and it works for almost any scanner. Your scanner is like a separate device from your printer and works from different software.
Software that separates legal from letter is bush league. You have to put it back together in the proper order most times. You're a pro now and need the right tool.
VueScan is the app built specifically for scanning and it will do many things in addition to scanning mixed paper sizes. One of the best features is that it eliminates
your scan hopper limits. Got a 50 page doc to scan but your scanner only holds 35 pages? No problem, you don't need to make two files. After you run your first 35 pages
through the scanner, VueScan will ask if you want to add more pages. Just click the SCAN+ icon and it will continue scanning the next 15 pages seamlessly.
Runs about $40-$60. The scan software that comes with you printer is so watered down and complicated. I don't work for them! I'm just an NSA like you but
I need my VueScan. Makes the job much easier and organized.