So I have a 99 accord and when I put the car in drive it hesitate about 5seconds till it takes gear and does the same thing when I put it in reverse. When I drive and come to a complete stops it feels like the transmission hits hard when goes back to 1st gear. Has anyone had this problem?? I've also just changed the transmission out and got one with 50,000 miles on it and still have the same issues.

 

have you checked the fluid level in your transaxle? if the level is fine (you check the level with the vehicle running in park or neutral) did you replace the torque converter as well as the transaxle?

if the fluid is good and the torque converter was replaced, your transaxle is going out. The sixth generation Accord's had terrible automatic transaxle's. Prior the the sixth gen, the fifth gen had one of the best ever built transaxle's from Honda.

 

Check all your pressure sensors are not leaking. If the gear changes are harsh or slam into gear, check your engine and transmission mounts. If they are worn they will allow excessive movement and when the trans engages it will not only feel delayed but will also be harsh.