If the squirrel cages aren't oriented the same way the original blower cages were oriented, you will get very little airflow through the vents. You have to look at the curve of the blades, and make sure the airflow is from the center of the cage straight out towards the evaporator. It can be installed so the air blows against the bottom of the housing (I did this once).

Other possibilities include blockage against the evap or the air inlet, HVAC hoses (but unlikely they would all be disconnected) or a vacuum flap problem (but some should default open). If the blower motor is all you worked on, the problem is probably somewhere there...

-anthony