Unfortunately when Blood was developed, scroll wheel wasn't a staple of computing hardware. So use of a scroll wheel was not part with the default software. There is an outside chance that an external mouse program like BMouse.exe could be written to give scroll wheel functionality, i is currently being maintained by SwissCM.

You can map to your third mouse button and on most mice this is generally the scroll wheel when you click it, rather than scroll with it.

You should be able to indicate between left and right shift/control/alt keys through setup.exe, rather than the in-game controller settings. You can also edit your blood.cfg file directly with a text editor like notepad. It is located in your blood installation directory. (ie. Program Files\GoG.com\One Unit Whole Blood\blood.ini)

I hope that helps a little.