Is there a way to mark several hundred old transactions as reconciled in one step?
There is no one step way to do this. The best way to do this is to set the view to show only unreconciled transactions sorted by date, select the earliest transaction you want to mark, hold down Ctrl+Shift. Hit M. You can hit M repeatedly or just hold it down to auto-repeat. Transactions will disappear–to reconciled status–pretty quickly, limited only by Money’s performance on your computer.