Winshield wiper transmission reset

I need help!! I had my wipers over extend past the A pillars so I replaced the wiper transmission assembly. The motor was fine. Now the wipers don't over extend anymore, but now the timing is all off. When I run the delay, the wipers are pausing in the up position instead of the down. Also, they crash into each other when the are turned off. I am at a loss on how to adjust them. Can anyone help? Thanks.