Misfire, flashing check engine lights, ABS flashing lights

I replaced the engine in my base model SUV. The dash board shows flashing check engine and flashing ABS lights, and the error codes are P0300, P0301, P0141, P0161. I have changed coils, plugs, OCV, tested the sensor behind the wheel caliper. Problem: the car is sluggish, it takes two cranks to start, when it moves in some gears it accelerates very well but once there is a gear change it drags for a bit until the it kicks down to a lower gear. Which I have to rev very high before the next gear takes over. Help!