It could be a failure of the selespeed to disengage the clutch fully. This would tie in with your symptoms of the gears clunking in when selecting first and reverse.
If the clutch is dragging it may be enough to dip the revs at tickover, when the aircon is running you have the added load of the compressor so the problem will seem worse.
I would ask them to have a look at the clutch actuator adjustment and also to check the hydraulic clutch fluid for air.
Also get them to make sure your selespeed has the latest software version as this was a known selespeed problem on early versions. A software upgrade has been released.