IMHO, if you want to encourage use of manual aiming, you need to do it earlier so that players could get accustomed to it by the final level. Because at current pace it's basically equivalent to introducing new mechanic at the end of the game. IDK how it should be implemented... One idea I have is add one more level, make weapons unlockable by progressing to the next level and make every level not beatable without manual aim. Or just disable autoaim entirely...
There also were moments when i tried to click tower upgrade and instead (missing mouse position by few pixels) was switching tower to manual aim.