Merge Academy - stuck with all high level merges

You have my sympathy.  I went through a spate of those, it was weeks of high end potions (actually still have 2 in m  orders as we speak).  As abbycattx said, try not to fill lesser orders, just keep plugging away at the higher end items.  I find it annoying when I'm trying to fill a higher order and the lesser orders blinks in the upper left corner, wanting me to complete it.  To avoid that, I move one item of the order to my storage cabinet, then take it back out when I have generated another of the same to merge with it.  Otherwise, there isn't much for it except patience and persistence.