If Ford are so adamant that Mondeo arm bolts should go from the top down, why are all Fiesta and escort ones fitted from the bottom up???
I've never fitted them down BUT i do fit a new bolt and locking nut - once in I cut the top of the bolt down so there is plenty of clearance for the gearbox. If you leave it std lenth then it'll touch.
What I gather is when you undo a Mondeo subframe you need alighnment pegs to get it aligned right though.