As for alignment use registration pins and you can get it perfectly aligned every time. Just add 2 or 3 “ears” to your layers with a registration hole, glue it up with the pins in place, then cut/sand/lathe the ears off when you’re making the final design. I use brass rods for registration and remove them once the glue is set, but you can use anything that’s handy — nails, dowels, even laser cut wooden pegs. I used this technique on a sword blade here:
There are two registration holes in the handle, and one “ear” is visible in the lower right of the blade near the tip:
In your case it might be simpler to extend the length of the blanks, you can trim or turn the excess length ( and the registration holes therein) away later in your process.
Also might be worth trying to remove the cut residue chemically instead of physically. Instead of sanding, perhaps use an alcohol wipe to clean the edges prior to gluing? I’ve never done any strength tests with before and after cleaning, but it might be worth a quick test to see if it helps. 2 copies of a quick test butt joint piece, clean one and not the other, glue em up, and then intentionally break them to see if there is a difference?
You have to scroll down to see where I broke a test butt joint here but I only tested it with a “dirty” edge.