Reads like a Vacuum problem.
The vents in the dash are held in their various positions by engine vacuum.
Default position is Defrost, so low or no vacuum will cause air to flow to Defrost vents.
Because engine vacuum is not consistent here is a vacuum reservoir that stores vacuum to hold these vents in position while engine is under load(low vacuum), if reservoir or vacuum line has a small leak then system simply runs out of vacuum during periods of longer low vacuum.
See if vents are switching to defrost vents at highway speeds.
As far as temp, AC system could be low on refrigerant.
A new motor can be installed without opening AC system but moving the AC lines around could have caused a leak.
Or if system was depressurized for the install then it should have had a new dry/accumulator installed when it was refilled, and it may need a top up.
Last edited by RonD; 08-18-2016 at 09:24 AM.