hi Richard
i think you've got a couple of issues confused;
there is no way any scanning software could have more control than PS, they may seem to offer some control, but that is just to make the user think they are user friendly/idiot proof
bit depth is not actually about image quality, it is more about how many colours can be described, if you are working on mono images, or even toned mono images, you are starting with an image that is already rendered in a restricted pallete
an image can look great on screen but print awful due to several factors; a screen image only needs 72 dpi at whatever is the screen size in pixels, whilst a printed image needs 300 dpi at the final print size
scanning should be done at the parametres that will be produce enough data for the requirements of the final image, it is a good idea to scan larger than is required but your scans are grossly too big, if my calculations are correct your files could render an image 2.4 x 1.35 metres
further to the above, these are huge amounts of data that will require huge files that will soon cause you handling and storage problems