Transmissions

Okay, I just replaced a burnt up tranny. I have the 3.1L V6. Before my car had 4 primary drive gears. Low= 1-2 Drive=3 and Over Drive=4. Since I replaced the tranny my low gear first gear does not engage unless I manually shift it into low upon attempting to move forward. Then second engages and the tranny will not downshift back into low first gear unless you re-manually do it. 2-3 work fine but then the trans will not shift up into overdrive at all. I am now only able to drive in 2 gears. If I reverse or just pull away in D or OD upon starting the car without shifting into low manually first. The car acts like it is taking off in second gear. Very slow and sluggish as if it has 0 torque. Any idea what could be causing this? Im lost and about to lose my mind with this car. I've already replaced 3-4 vacuum lines. Would just like to know what else it could be? Any help would be appreciated.