What box have you got? a cable shift box i take it.
It can be adjusted, but special tools are needed.
There is a basic adjustment, but unfortunately i won't be able to look it up for a couple of days as its packed, i'm moving house of Thursday.
In all honesty if there any niggles with it, contact the garage, they sound like a bunch of useless muppets, don't let them get away with sub standard work.
Did they replace the engine by the way?